Abstract
Soil health is the capacity to support the production of food, feed, and fiber while delivering other essential ecosystem services. We suggest key soil health indicators and examine the three-way interactions between mineral fertilizer, crop productivity, and soil health. Given the long history of soil nutrient depletion in Sub-Saharan Africa, we conclude that mineral fertilizer use, as a core component of integrated soil fertility management, must increase and be co-applied with organic inputs to increase productivity and fertilizer use efficiency and restore and sustain soil health.
Introduction
The urgent need to increase agricultural production in sub-Saharan Africa (SSA) to ensure food and nutrition security for its growing population has been widely acknowledged1,2. Pressure on land in SSA is aggravated by increasing global demand for agricultural products such as cocoa or oil palm3. If intensification of crop production is unsuccessful and massive cropland expansion is to be avoided, SSA will become much more reliant on cereal imports than it is today4. Despite the overall disappointing agricultural production statistics across the continent, some African countries have moved toward a trajectory similar to Asia, achieving higher crop yields on the same land area through the increased use of mineral fertilizer, henceforth referred to as ‘fertilizer’, sometimes with rates reaching the target of 50 kg of fertilizer nutrients per hectare, proposed by the Abuja 2006 Fertilizer Summit5 (Fig. 1).
Relative changes in grain yield and land area used for growing cereals (rice, wheat, maize, barley, sorghum, and millet) in Asia and Africa (left)75 and changes in selected countries of sub-Saharan Africa for maize (right). The black markers in the right graph refer to the period 2006–2010, the period following the Abuja Fertilizer Summit. Data shown in the right graph are five-year averages for 1961–2020 and the 3-year average for the period 2021–2023. The average of 1961–1965 was set as 100. Source: FAOSTAT76.
Acknowledging that progress over the past two decades has been variable and that new, more comprehensive strategies are needed to improve fertilizer use and soil health in Africa, the African Fertilizer and Soil Health Summit was held in Nairobi in 2024. The summit culminated in the adoption of the Nairobi Declaration and a 10-year action plan6 to revitalize the concept of soil health and enhance agricultural productivity across Africa. The plan calls for more context-specific, integrated approaches to soil fertility management, embracing the principles of integrated soil fertility management (ISFM)7.
Soil degradation is a major factor underlying the low crop productivity and high prevalence of malnutrition in SSA8. Soil degradation in Africa is largely driven by suboptimal application and management of nutrients, resulting in a downward spiral of poor crop grain and biomass yields, resulting in less organic inputs and soil cover. Degradation triggers a decline in soil biological, chemical, and physical quality, and its capacity to support crop production and regulate environmental functions—together referred to as soil health9. Decades of soil nutrient mining—continuous cropping with few nutrient inputs has severely degraded the productive capacity of vast agricultural areas in SSA, making it the only global region with persistently negative nutrient balances that have worsened over time10 (Fig. 2). Increasing crop productivity to meet current and future food needs while preserving soil health will not be possible without increased and efficient use of all possible nutrients, with critical contributions from mineral fertilizers4,11.
a Cropland P inputs and outputs for Africa and b cropland P balance for its sub-regions for the period 1960–2020. Source: FAOSTAT76; Ludemann et al.77.
The main objectives of this paper are: (i) to illustrate the fundamental role of soil health in supporting sustainable agriculture; (ii) to review the evidence on how fertilizer use interacts with soil health; and (iii) to recommend how fertilizer can be used more efficiently to improve agricultural productivity and soil health. We focused on upland, rainfed annual cropping systems, since these are the most common farming systems managed by smallholder farmers in SSA (Table 1). While we recognize that the recommendations for these systems may not apply to irrigated lowland agriculture or perennial systems, most smallholder farmers in SSA and in other parts of the tropical regions, including those with part of their farm under perennials or lowland rice, rely heavily on these rainfed systems for their food requirements and livelihoods.
Conceptualization of soil health
Description of functions and properties
Soil health is commonly defined as the continued capacity of soil to function as a vital living system, within ecosystem and land-use boundaries, to sustain biological productivity, promote the quality of air and water environments, and maintain plant, animal, and human health12. In the context of agricultural soils, it refers to the capacity to support the production of food, feed, and fiber in amounts and quality sufficient to meet human and animal needs while delivering other ecosystem services that are essential for maintaining the quality of life for humans and the conservation of biodiversity13. To deliver those goods and services, soils perform a number of essential functions, including (i) regulation of water flows and storage, (ii) storage, regulation, and recycling of nutrients, (iii) provision of physical stability and support, (iv) provision of habitat and energy for soil organisms, (v) filtration and buffering of potential pollutants, and (vi) mitigation of climate change14. Several soil properties underpin these functions, classified as chemical, physical, and biological properties.
Soil chemical properties include total nutrient stocks, amount of available or exchangeable nutrients, acidity and buffering capacity, cation and anion capacity, soil organic matter content, base saturation, and salinity. Soil physical properties include color, texture, structure, porosity, bulk density, aggregate stability, and temperature. Soil biological properties include abundance, diversity, and activity of soil biota, including macro-, meso-, and microfauna, or proxies for the processes they perform in soil (e.g., carbon (C) or nitrogen (N) mineralization potential, and soil enzyme activities). Standard methods for assessing chemical and physical properties have been available for many decades. Further, the chemistry, physics, and biology of soils are interdependent—for example, macrofauna such as earthworms and termites are key to porosity. How these properties are affected by inherent soil conditions or management practices and their interpretation in relation to specific soil functions is relatively well understood15,16. Despite the importance of biological properties for specific soil functions, biological soil health indicators have been underutilized, due to the complexity of the soil biotic communities and challenges with establishing causal relationships between biological properties and specific functions9 except for keystone species linked to specific soil processes or functions16,17. Future research needs to elucidate the role of soil biota in soil health assessment, including the support of soil functions for production and ecosystem services.
Because of the diverse functions regulated by soil and the large number of soil properties that interact with those functions, a practical indicator framework for soil health needs to be constructed based on indicators that have causal relationships with key functions that can be measured over time and space18. For instance, while the critical soil functions in a natural ecosystem do not include sustaining crop production, this function is obviously of utmost importance for agroecosystems. Hence, several soil indicators and their critical values in natural ecosystems are, by definition, not valid targets for healthy soils under agriculture.
Indicators of soil health from an agronomic perspective
Here, we focus on soil health in support of crop production, which requires, besides light and carbon dioxide, sufficient and timely access to water, a sufficient and timely amount of nutrients with the right composition, and proper root development to recover nutrients and water. It also requires sufficiently low levels of toxic elements that may hamper plant growth, such as exchangeable aluminum (Al), or soil-based pests and diseases, such as root knot nematodes.
We suggest that the key indicators to sustain crop production are soil organic matter (SOM), available P and exchangeable K, soil acidity, expressed through its pH, and bulk density. Available N is highly dynamic in the soil, making it an unreliable indicator, but SOM provides a good proxy for total N. Common C:N:P ratios of agricultural soil are around 100:10:119, and 1 ton of SOM contains about 600 kg of C, 60 kg of N, and 6 kg of P, all gradually released through decomposition. Soil organic matter is not only a source of nutrients but also a temporary store through its cation exchange properties20 that also determine the proton buffering capacity of SOM. Additionally, SOM influences soil structure and thereby bulk density and soil porosity and thus water storage, movement, and root growth21. The amount of SOM and the potential of soil to accumulate SOM are strongly influenced by the amount and reactivity of the clay (and silt) particles in the soil22. As such, determination of critical thresholds for SOM content in relation to soil health must take into consideration specific soil texture and mineralogy classes.
Phosphorus (P) and potassium (K) are the most limiting plant nutrients besides N and are required by all crops in substantial quantities, with the root and tuber crops, as well as bananas, requiring particularly large amounts of K. Moreover, for legumes to effectively fix considerable amounts of N from the atmosphere, sufficient P is required23. Soil acidity influences the availability of nutrients with direct impact on crop growth 24 and regulates the amount of exchangeable Al or manganese (Mn), which are toxic and hinder crop growth25.
Soil bulk density is a critical physical property influencing root growth, water infiltration and retention, and soil aeration. For example, high bulk density indicates compacted soil, which restricts root penetration and expansion. It can also lead to reduced water infiltration and increased surface runoff, which limits water availability to plants. At the same time, high bulk density will also limit nutrient availability by inducing anaerobic conditions, which will reduce nutrient mineralization and favor gaseous losses of N as N2O and N226.
Thresholds for soil properties can be broadly categorized into three types: ‘killer’ thresholds, where exceeding a critical limit causes immediate and severe loss of function; ‘soft’ thresholds, where functionality declines gradually once crossed; and ‘more is better’ thresholds, where increasing levels consistently improve the soil function without a clearly defined upper or lower limit. For example, on soils with substantial Al contents, soil acidity has a killer threshold at pH values of 5.5, below which Al saturation can exceed 15%, thus hampering crop growth27. At the other extreme, soil pH values above 9 limit the availability of specific nutrients such as P, Mn, Zn, or B28. Available P and exchangeable K have soft thresholds above which there are no limitations to crop growth, and below which crop growth is reduced but not ceased. As for SOM, there is no easily identifiable minimum threshold, but in general, more SOM is better for soil health and crop productivity.
In addition to the need for specific indicators to assess soil health, three other key factors must be considered in a soil health indicator framework: (i) spatial heterogeneity—some soil properties can vary significantly over short distances, particularly in densely populated areas with absence of fallow land29; (ii) rate of change—some indicators change rapidly (e.g., changes in available nutrients), while others change slowly, especially when these are measured against a relatively large background (e.g., changes in SOM); and (iii) measurement costs— assessing indicators over large areas of land can be expensive although the availability of spectroscopic methods have succeeded in substantial reductions in cost for some soil health indicators. As an alternative to direct measurement, changes in crop and soil management practices can be evaluated as proxies for expected changes in key soil health indicators through empirical or mechanistic modeling approaches30.
Finally, much of SSA is characterized by highly weathered soils, which often result in more than one nutrient deficiency, a contrast to most soils in the northern hemisphere. Varying proportions of the soils in SSA suffer from secondary and micronutrient limitations, including S or Zn31 and this can be exacerbated when focusing solely on NPK fertilizer. Obviously, addressing these location-specific deficiencies is crucial for resolving soil health and enhancing crop productivity.
Conceptual framework linking fertilizer use to soil health
The conceptual framework relating fertilizer use to soil health includes the main components of cropping systems and their interactions, along with management interventions and inherent soil properties (Fig. 3). Crop production levels are the result of yield-defining (radiation, temperature, and CO2), yield-limiting (water, nutrients), and yield-reducing factors (biotic factors, pollutants)32. Soil health influences both yield-limiting factors (water (oxygen) and nutrients) and yield reducing factors (pH, pest/diseases and pollutants), while fertilizer and lime can (i) alleviate nutrient-limiting factors, (ii) increase crop yields and thus residues and SOM or soil health, and (iii) directly affect soil health (e.g., through increased nutrient availability and influences on soil pH).
Bold boxes are system components, while dashed ovals present management interventions. Dashed light boxes are inherent soil properties affecting soil health. Arrows present processes connecting the components, while losses are presented as clouds connected with dashed arrows.
Nutrients can be supplied either from fertilizers, manure, compost, crop residues, biological N fixation or derived from soil nutrient stocks in the form of SOM or weatherable minerals. Water availability, either through rainfall or irrigation, and soil aeration status mirror each other, and the correct balance between the two is affected by soil structure, which is influenced by crop residue or manure application and land preparation33,34. Soil organic matter is increased with the application of crop residues, either directly or after passage through livestock as manure35.
The above processes are affected by specific inherent soil properties, affected by their position in a landscape. Soil depth, limited by physical barriers such as hardpans or a high water table, affects the soil volume that plant roots can explore for nutrients and water. Soil texture affects the potential of soils to form soil structure, with sandy soils having limited scope for the formation of a stable structure, while clay type affects the potential to bind organic matter, with 1:1 clays having less potential than 2:1 clays22,36. In general, soils in SSA are mostly highly weathered and dominated by 1:1 clays with limited capacity to store both organic matter and nutrients in an exchangeable form37. Additionally, the reserve of weatherable minerals in many soils of SSA is small37 constituting a major difference with the much younger soils in the northern hemisphere.
Fertilizer use and its impact on crop production and soil health
Fertilizer use and crop yields
National-level data and other evidence, such as soil nutrient balances, show that fertilizer use is necessary to increase and sustain crop yields in SSA11,38,39. There are many ways to assess fertilizer use efficiency (FUE)40 each with its own requirements and limitations41. Among these, agronomic use efficiency (AE) is a commonly used indicator due to its ease of assessment. Agronomic use efficiency of N (AE-N) is calculated as (Eq. 1):
However, the assessment of AE requires data on crop performance in the absence of fertilizer (control treatment), which is often missing in surveys, national statistical databases, and farmer trials. In such cases, partial factor productivity (PFP) of fertilizer (Eq. 2) is used as an alternative, estimated as the ratio of yield to fertilizer nutrients applied, for instance, for N fertilizer:
Other approaches for estimating FUE exist, but they typically require direct measurements of nutrient uptake, limiting their use to experimental field studies.
African farmers generally achieve highly variable and relatively low FUE values, resulting in marginally profitable or unprofitable fertilizer use42,43. In contrast, researchers’ experiments consistently report substantially higher FUE values44. To maximize FUE, fertilizer application must follow the ‘4 R nutrient stewardship’ principles—applying the right source, at the right rate, at the right time, and in the right place45. Moreover, other management practices and decisions are often equally important to maximize FUE, including the choice of germplasm and planting dates, the combined application with organic inputs, the deployment of other amendments (e.g., lime to address soil acidity-related constraints), or other practices (e.g., weed, pest, and disease management or sub-surface plowing in case of hardpans), as conceptualized through the ISFM paradigm7,8.
There is ample evidence that maintaining and improving SOC leads to higher FUE. A clear example comes from a 3-year study on millet35,46, which found significantly higher FUE in the more fertile fields near the farm homestead compared to the less fertile fields further away. Additionally, integrating mineral fertilizers with organic inputs, as part of ISFM, has been shown to improve FUE by alleviating key nutrient uptake constraints35. In general, the effects of mineral fertilizer and organic inputs are additive with moderate application rates, while negative interactions between both inputs are exceptional47.
Fertilizer use and soil health
Fertilizer application can affect soil health in both positive and negative ways. For example: (i) application of P and K-based fertilizers can increase stocks of available P and K beyond the season of application, or (ii) fertilizers can increase crop yields and thus allow return of larger amounts of crop residues to the soil, thereby potentially enhancing SOM content and quality. Furthermore, ammonium-based fertilizer (e.g., urea, ammonium sulfate) can gradually increase soil acidity through the release of protons during the nitrification process.
When P fertilizers are applied to soil, a portion of the P is adsorbed onto soil minerals or precipitated into less soluble forms. Over time, some of this sorbed P can desorb back into the soil solution, becoming available for plant uptake in subsequent seasons. The desorption rate depends on soil properties such as pH, clay content, and organic matter48. Several studies in SSA have shown that both natural rock phosphate and single superphosphate fertilizers have significant residual or ‘legacy’ effects, improving soil fertility and increasing cereal crop yields49. Potassium applied as fertilizer is more mobile in the soil than P but leaches less than nitrate, except in sandy or highly weathered soils50. In medium- and heavy-textured soils, a significant portion of applied K remains in the root zone and is available for subsequent crops. In soils with illite, vermiculite, or smectite clays, K+ ions can be trapped between clay layers. Over time, as soil moisture and temperature fluctuate, some of the trapped K⁺ slowly re-enters the soil solution, making it available for plant uptake in subsequent seasons51.
Theoretically, fertilizer use can enhance SOC by boosting crop plant productivity and thereby increasing C inputs to the soil through greater biomass returns52. However, a review of published meta-analyses on the effect of mineral fertilizer on SOM53 found only one meta-analysis covering experiments in SSA54, which showed no significant effects of fertilizer application on SOM (Fig. 4). This could be the result of low fertilizer application rates and/or sub-optimal associated agronomic factors, further aggravated by the removal of crop residues in many African farming systems for alternative uses. Similarly, results from four long-term experiments in Kenya35,55 and one in the Ivory Coast56 indicate that while mineral N fertilizer is crucial for short-term maize yield improvements, its long-term use without organic inputs does not increase SOC. On the other hand, Zingore et al.57 found that commercial farmers in Zimbabwe, through the use of mineral fertilizers and hybrid maize varieties, and recycling of crop residue, maintained SOC contents almost double those in communal farming systems on similar soils without external inputs. Ultimately, it is likely that to increase SOC, both internally generated (e.g., crop residues) and external organic inputs (e.g., manure, compost) may be required. Options also exist to ‘internalize’ the production of organic matter, e.g., through agroforestry options or herbaceous legume intercrops or rotations, but the uptake and scalability of such interventions face other challenges beyond the scope of this paper58.
Points represent the mean effect size, and error bars represent the confidence interval. Numbers represent paired data used in a given meta-analysis. N: nitrogen; P: phosphorus; and K: potassium. Data from the evidence map of Beillouin et al.53.
Under unbalanced fertilization, some studies have shown that mineral fertilizers can reduce SOC through priming effects in the rhizosphere—a process whereby plants and microbes decompose native SOM to access limiting nutrients59. This phenomenon is often driven by stoichiometric imbalances, especially in micronutrients, prompting microbial mining of SOM to satisfy nutritional demands.
A specific concern of soil health for SSA is soil acidity60. The dominance of weathered soils in SSA implies a small reserve of weatherable minerals and a limited buffering capacity against pH changes61. Given the current limited use of lime, care should be taken when selecting the type of fertilizer, as the application of ammonium-containing fertilizers may aggravate the situation29. Ammonium-based fertilizers (e.g., urea, ammonium sulfate) increase soil acidity over time through the process of nitrification, which releases protons (H⁺) in the soil solution. Additionally, H⁺ displaces cations (Ca²⁺, Mg²⁺, ānd K⁺), which are subsequently leached, further acidifying the soil. Over time, increased acidity can lead to aluminum (Al³⁺) and manganese (Mn²⁺) toxicity, harming plant roots62. Application of lime can mitigate this acidifying effect, but its economic and agronomic effects need a long-term perspective63.
Crop productivity and soil health
Increased crop productivity generates larger amounts of crop residues, including roots, which can enhance soil health. On average, a 1.3% annual increase in crop grain yields is associated with a 0.4% annual increase in SOC, based on studies from Africa, Asia, and Latin America (Fig. 5). The large scatter in the data results indicates that several other factors besides increased crop productivity affect changes in SOC, suggesting the importance of additional management practices to ensure that increased crop yields and biomass productivity have a positive effect on soil health. Several studies55 have shown that farmyard manure is more effective in stabilizing SOC than fresh crop residues. Farmyard manure contains partially decomposed organic matter, including humified compounds that are more resistant to microbial breakdown, also forming stable soil aggregates that protect SOC from decomposition22.
Crop species: B, beans; C, cassava; M, maize; P, sweet potatoes; R, rice; S, soybean; s, sorghum; W, wheat. Field experiment regions: Africa (black); Asia (green); and Latin America (blue). The solid line is the standard major axis regression for all data points (n = 151, Spearman’s rank correlation: y = 0.495 + 3.21x; r = 0.205, P < 0.012). Source: Soussana et al.78.
Moinet et al.64 reviewed 21 meta-analyses and found that the effects of increasing SOC on crop yields are highly variable, ranging from negative to neutral to positive. SOC sequestration does not universally improve yields, and any positive effects are highly context dependent. Factors like soil texture, climate, and nutrient availability significantly influence yield responses, and establishing causality between SOC stocks and crop yields is therefore challenging. Agricultural practices that increase SOC may also improve yields, meaning their correlation over time does not necessarily imply a direct causal relationship. Even if a causal link exists, it is difficult to determine whether SOC influences yield or vice versa. Calibrated crop models tailored to specific conditions could help address this uncertainty52.
Crop residues help mitigate this by returning essential cations like calcium (Ca²⁺), magnesium (Mg²⁺), and potassium (K⁺) to the soil as they decompose. This also helps neutralize soil acidity by replacing hydrogen (H⁺) and aluminum (Al³⁺) ions on soil exchange sites. However, when crops remove more cations (Ca²⁺, Mg²⁺, K⁺) than those replenished through residue decomposition, soil acidification may occur over time65.
Integrated soil fertility management
The co-application of mineral fertilizers with organic inputs is a foundational principle of ISFM7 because neither input alone can sustainably support crop productivity and soil health in smallholder systems of SSA. Organic inputs such as crop residues, manure, and compost increase SOC, contribute to improved soil structure, water retention, cation exchange capacity, and biological activity, and help buffer soils against acidity and nutrient losses. However, when applied at quantities typically available on smallholder farms, they rarely release sufficient nutrients to meet crop demand11. Mineral fertilizers, in contrast, provide concentrated and immediately available nutrients that enable rapid yield increases but are most effective when soil physical and biological constraints are alleviated through organic matter management.
Evidence from ISFM research shows that positive interactions between mineral and organic nutrient sources frequently enhance agronomic use efficiency by improving nutrient capture and conversion efficiency, particularly on degraded or poorly responsive soils54. Fertilizer application can also stimulate biomass production, thereby increasing the availability of crop residues that could have a positive impact on SOC and protect soils against erosion, if produced and retained in sufficient quantity. On the other hand, sustained application of organic inputs can rehabilitate degraded soils and restore their responsiveness to mineral fertilizers. These complementary effects demonstrate that integrated management of mineral fertilizers and organic resources is essential not only for maximizing short-term yield responses but also for rebuilding soil fertility and ensuring long-term sustainability of cropping systems in SSA.
Economic realities
Although fertilizers are a key component of sustainable food systems and essential for maintaining soil health, their widespread use in Africa heavily relies on policy support66. Adoption and application rates among smallholder farmers in SSA remain far below optimal, despite many initiatives to promote fertilizer use67. The prime cause for low adoption of fertilizer is its high cost relative to prices that farmers get for their produce. Crop response to sole application of fertilizers is poor without complementary good agronomic practices, leading to low, highly variable, and even negative economic viability43. In addition, a range of factors influence fertilizer use, including household and farm characteristics, social and human capital, type of crops produced, credit access, off-farm income, regular labor availability, and farmers’ perception of the effects of fertilizers on soil fertility68. Moreover, biophysical conditions, such as rainfall patterns and soil type, are important; in particular, the high risk of crop failure resulting from low or erratic rainfall is a strong disincentive to investing in fertilizers for subsistence crops69.
Crop yields in SSA remain well below what is attainable given the environmental conditions and available technologies, referred to as the ‘agronomic’ yield gap. Even though it may be technically feasible to reduce yield gaps in many regions of SSA, it is not always economically viable for farmers to pursue higher crop yields. For example, Bonilla-Cedrez et al.70 showed for maize that (i) the average economic yield gap (the difference between current yield and those that would maximize profit) was about 25% of the agronomic yield gap; (ii) although maize yields could, in theory, be profitably doubled, actual economic incentives are weak due to unfavorable and highly variable input-to-output price ratios; and (iii) risks associated with erratic seasonal rainfall further discourage investment in fertilizer.
Farmers who grow high-value crops or crops under irrigation are more likely to invest in fertilizers and other soil health-enhancing management practices as a way to increase profitability. While investments are generally lower for traditional staple food crops, rising food market prices, often driven by their use as raw materials in processing industries (e.g., cassava for flour), can encourage farmers to adopt fertilizers. Land is a key factor of production, and farmers with larger farm sizes are generally more inclined to invest in fertilizers and soil health-enhancing practices. In addition, secure land tenure (whether in terms of access, use, or ownership) also encourages investment in fertilizer and other technologies, in contrast to situations of insecure tenure, which tend to discourage long-term investment in cropland71,72. Furthermore, land ownership often enables access to credit, an important factor for investments in fertilizers.
Farmers’ age, gender, and education level are important mediating factors that shape their knowledge, ability, decision-making capacity, preferences, and risk tolerance, all of which influence the adoption of agricultural technologies. Lower adoption of fertilizer use by women farmers may be attributed to differences in technology preferences, cultural norms, and the suitability of agricultural tasks typically performed by women73. Furthermore, women’s adoption of technologies is frequently constrained by access to inputs, extension support, and access to credit and markets. They may also lack complementary resources, especially land and labor.
Concluding remarks
There is a broad consensus that agricultural productivity in SSA can and must increase to meet food needs, while expansion of arable land, deforestation, and loss of biodiversity must be avoided. Achieving this requires fertilizer and organic inputs, in combination with good agronomic practices, improved seeds, and other amendments, core components of the ISFM approach. Building soil health or regenerating degraded soils is a long-term process, while the loss of soil health is rapid when nutrients and SOC are not replenished. Building soil health will not be possible without the use of fertilizers, as available organic inputs provide only a part of the required nutrients, and their transfer from one location to another leads to soil depletion and degradation elsewhere.
A major barrier to the adoption of soil health-restoring practices by smallholder farmers is the time lag before visible benefits appear. In the absence of incentives and driven by short-term economic rationale, farmers tend to favor interventions that yield immediate returns. With the broadening of soil fertility management recommendations beyond mineral fertilizers, practical tools that translate complex information into actionable guidance are needed. Digitally enabled tools, together with scaling models and bundled services, that include good agronomic practices with socio-economic drivers like credit access, can help bridge this gap, facilitating farmers’ access to balanced sets of agro-inputs, advice, and technologies. Policy interventions are also essential, creating an enabling environment for the adoption of fertilizer and soil health management recommendations, including institutional incentives, smart subsidies, and knowledge transfer through an effective extension system. In this context, it is crucial to redesign fertilizer subsidy programs beyond reducing cost toward actively promoting soil health outcomes.
Instead of a blueprint approach, soil health recommendations should always be tailored to local conditions. Several approaches can be used to develop optimal fertilizer recommendations that account for crop nutrient requirements and field-specific soil characteristics. This involves assessing the soil fertility status of individual fields. New data and analytical tools now allow for the development of site-specific recommendations at scale. In particular, recent tools based on artificial intelligence can improve the development and delivery of hyper-local advisory services tailored to a single field on a single farm74.
While low crop yields and high agronomic yield gaps are linked to biophysical factors and management, it is the economic yield gap, shaped by input and output prices, that ultimately determines farmers’ investment decisions and returns on investment in fertilizer or organic input use. While profitability is a key driver for adoption, many other factors affect the uptake of appropriate fertilizer and soil health recommendations, including farmers’ production objectives and resource endowment, land tenure, and access to markets.
Regardless of the agro-ecological complexity, to enhance soil health while retaining economic viability, the combined use of mineral fertilizers with organic inputs and complementary good agronomic practices must be catalyzed through policy and other incentives to ensure a sustainable provision of food and other ecosystem services. The action plan, as laid out by the Fertilizer and Soil Health Summit of the African Union6 proposes critical measures to achieve increased and profitable crop yields and soil health.
Data availability
No datasets were generated or analyzed during the current study.
References
Luan, Y., Cui, X. & Ferrat, M. Historical trends of food self-sufficiency in Africa. Food Secur. 5, 393–405 (2013).
Google Scholar
Van Ittersum, M. K. et al. Can sub-Saharan Africa feed itself? Proc. Natl. Acad. Sci. USA 113, 14964–14969 (2016).
Google Scholar
Kongor, J. E., Owusu, M. & Oduro-Yeboah, C. Cocoa production in the 2020s: challenges and solutions. CABI Agric. Biosci. 5, 102−130 (2024).
van Ittersum, M. K. et al. Prospects for cereal self-sufficiency in sub-Saharan Africa. In Proceedings of the National Academy of Sciences of the United States of America, vol. 122 (National Academy of Sciences, 2025).
AfDB. Abuja declaration. https://www.afdb.org/en/topics-and-sectors/initiatives-partnerships/africa-fertilizer-financing-mechanism/about-affm/abuja-declaration (2006).
African Union. Africa fertilizer and soil health action plan. https://www.fertilizer.org/wp-content/uploads/2024/06/Action-Plan-Fertilizer-and-Soil-Health-_E.pdf (2024).
Vanlauwe, B. et al. Integrated soil fertility management: operational definition and consequences for implementation and dissemination. Outlook Agric. 39, 17–24 (2010).
Google Scholar
Vanlauwe, B., Six, J., Sanginga, N. & Adesina, A. A. Soil fertility decline at the base of rural poverty in sub-Saharan Africa. Nat. Plants 1, 15101 (2015).
Google Scholar
Lehmann, J., Bossio, D. A., Kögel-Knabner, I. & Rillig, M. C. The concept and future prospects of soil health. Nat. Rev. Earth Environ. 1, 544–553 (2020).
Google Scholar
Zou, T., Zhang, X. & Davidson, E. A. Global trends of cropland phosphorus use and sustainability challenges. Nature 611, 81–87 (2022).
Google Scholar
Falconnier, G. N. et al. Increased mineral fertilizer use on maize can improve both household food security and regional food production in East Africa. Agric. Syst. 205, 103588 (2023).
Google Scholar
Doran, J. W., Sarrantonio, M. & Liebig, M. A. Soil health and sustainability. Adv. Agron. 56, 1–54 (1996).
Google Scholar
Kibblewhite, M. G., Ritz, K. & Swift, M. J. Soil health in agricultural systems. Philos. Trans. R. Soc. B 363, 685–701 (2008).
Google Scholar
Banwart, S., Nikolaidis, N., Peacock, C. & Sparks, D. Soil functions: connecting Earth’s critical zone. Annu. Rev. Earth Planet Sci. 47, 333−359 (2018).
Arshad, M. A. & Coen, G. M. Characterization of soil quality: physical and chemical criteria. Am. J. Altern. Agric. 7, 25–31 (1992).
Google Scholar
Hartmann, M. & Six, J. Soil structure and microbiome functions in agroecosystems. Nat. Rev. Earth Environ. 4, 4–18 (2023).
Google Scholar
Giller, K. E., Beare, M. H., Lavelle, P., Izac, A.-M. N. & Swift, M. J. Agricultural intensification, soil biodiversity and ecosystem function. Appl. Soil Ecol. 6, 3–16 (1997).
Google Scholar
Bünemann, E. K. et al. Soil quality—a critical review. Soil Biol. Biochem. 120, 105–125 (2018).
Google Scholar
Zheng, S. et al. Stoichiometry of carbon, nitrogen, and phosphorus in soil: effects of agricultural land use and climate at a continental scale. Soil Tillage Res. 209, 104903 (2021).
Google Scholar
Helling, C. S., Chesters, G. & Corey, R. B. Contribution of organic matter and clay to soil cation-exchange capacity as affected by the pH of the saturating solution. Soil Sci. Soc. Am. J. 28, 517–520 (1964).
Google Scholar
Jarvis, N. et al. Interactions between soil structure dynamics, hydrological processes, and organic matter cycling: A new soil-crop model. Eur. J. Soil. Sci. https://doi.org/10.1111/ejss.13455 (2024).
Six, J., Conant, R. T., Paul, E. & Paustian, K. Stabilization mechanisms of soil organic matter: implications for C-saturation of soils. Plant Soil 241, 155–176 (2002).
Google Scholar
Vanlauwe, B., Hungria, M., Kanampiu, F. & Giller, K. The role of legumes in the sustainable intensification of African smallholder agriculture: lessons learnt and challenges for the future. Agric. Ecosyst. Environ. 284, 106583 (2019).
Wood, M. & Litterick, A. M. Soil health—what should the doctor order? Soil Use Manag. 33, 339–345 (2017).
Google Scholar
Kidd, P. S. & Proctor, J. Why plants grow poorly on very acid soils: are ecologists missing the obvious? J. Exp. Bot. 52, 791–799 (2001).
Google Scholar
Shah, A. N. et al. Soil compaction effects on soil health and crop productivity: an overview. Environ. Sci. Pollut. Res. 24, 10056–10067 (2017).
Google Scholar
Kamprath, E. J. Exchangeable aluminum as a criterion for liming leached mineral soils. Soil Sci. Soc. Am. J. 34, 252–254 (1970).
Google Scholar
Barrow, N. J. & Hartemink, A. E. The effects of pH on nutrient availability depend on both soils and plants. Plant Soil 487, 21–37 (2023).
Google Scholar
Vanlauwe, B. & Giller, K. E. Popular myths around soil fertility management in sub-Saharan Africa. Agric. Ecosyst. Environ. 116, 34–46 (2006).
Google Scholar
Nziguheba, G. et al. Assessment of sustainable land use: linking land management practices to sustainable land use indicators. Int. J. Agric. Sustain. 20, 265–288 (2022).
Google Scholar
Kihara, J. et al. Application of secondary nutrients and micronutrients increases crop yields in sub-Saharan Africa. Agron. Sustain. Dev. 37, 25 (2017).
Google Scholar
van Ittersum, M. K. & Rabbinge, R. Concepts in production ecology for analysis and quantification of agricultural input-output combinations. Field Crops Res. 52, 197–208 (1997).
Google Scholar
Eze, S. et al. Impacts of conservation agriculture on soil structure and hydraulic properties of Malawian agricultural systems. Soil Tillage Res. 201, 104639 (2020).
Google Scholar
Shumba, A. et al. Mulch application as the overarching factor explaining increase in soil organic carbon stocks under conservation agriculture in two 8-year-old experiments in Zimbabwe. SOIL 10, 151–165 (2024).
Google Scholar
Laub, M. et al. Managing soil organic carbon in tropical agroecosystems: evidence from four long-term experiments in Kenya. SOIL 9, 301–323 (2023).
Google Scholar
Feng, W., Plante, A. F. & Six, J. Improving estimates of maximal organic carbon stabilization by fine soil particles. Biogeochemistry 112, 81–93 (2013).
Google Scholar
Ito, A. & Wagai, R. Global distribution of clay-size minerals on land surface for biogeochemical and climatological studies. Sci. Data 4, 170103 (2017).
Google Scholar
Stoorvogel, J. J., Smaling, E. M. A. & Janssen, B. H. Calculating soil nutrient balances in Africa at different scales. Fertilizer Res. 35, 227–235 (1993).
Google Scholar
Kihara, J. et al. Understanding variability in crop response to fertilizer and amendments in sub-Saharan Africa. Agric. Ecosyst. Environ. 229, 1–12 (2016).
Google Scholar
Scientific Panel on Responsible Plant Nutrition. Defining Nutrient Use Efficiency in Responsible Plant Nutrition. www.sprpn.org (2023).
Ladha, J. K. et al. Efficiency of fertilizer nitrogen in cereal production: retrospects and prospects. in Advances in Agronomy vol. 87, pp 85–156 (Academic Press, 2005).
Jayne, T. S., Mason, N. M., Burke, W. J. & Ariga, J. Review: taking stock of Africa’s second-generation agricultural input subsidy programs. Food Policy 75, 1–14 (2018).
Google Scholar
Adzawla, W. et al. Characterization of farmers and the effect of fertilization on maize yields in the Guinea Savannah, Sudan Savannah, and Transitional agroecological zones of Ghana. EFB Bioecon. J. 1, 100019 (2021).
Google Scholar
Chikowo, R. et al. Nitrogen and phosphorus capture and recovery efficiencies, and crop responses to a range of soil fertility management strategies in sub-Saharan Africa. Nutr. Cycl. Agroecosyst. 88, 59–77 (2010).
Google Scholar
Zingore, S. & Johnston, A. The 44R Nutrient Stewardship in the context of smallholder agriculture in Africa. In Agro-Ecological Intensification of Agricultural Systems in the African Highlands (eds Vanlauwe, B., Van Asten, P. & Blomme, G.) pp 77–84 (Routledge, 2013).
Fofana, B., Wopereis, M. C. S., Bationo, A., Breman, H. & Mando, A. Millet nutrient use efficiency as affected by natural soil fertility, mineral fertilizer use and rainfall in the West African Sahel. Nutr. Cycl. Agroecosyst. 81, 25–36 (2008).
Google Scholar
Vanlauwe, B. et al. Agronomic use efficiency of N fertilizer in maize-based systems in sub-Saharan Africa within the context of integrated soil fertility management. Plant Soil 339, 35–50 (2011).
Google Scholar
Nwoke, O. C. et al. Assessment of labile phosphorus fractions and adsorption characteristics in relation to soil properties of West African savanna soils. Agricult. Ecosyst. Environ. 100, 285–294 (2003).
Google Scholar
Nakamura, S. et al. Residual effects of direct application of Burkina Faso phosphate rock on rice cultivation in Ghana. Nutr. Cycl. Agroecosyst. 106, 47–59 (2016).
Google Scholar
Schroth, G. & Sinclair, F. L. Trees, crops, and soil fertility: concepts and research methods. in Trees, Crops and Soil Fertility: Concepts and Research Methods (eds. Schroth, G. & Sinclair, F. L.) pp 151–166 (CABI Pub., Wallingford, 2003).
Stanford, G. Fixation of potassium in soils under moist conditions and on drying in relation to type of clay mineral. Soil Sci. Soc. Am. J. 12, 167–171 (1948).
Google Scholar
Couëdel, A. et al. Long-term soil organic carbon and crop yield feedbacks differ between 16 soil-crop models in sub-Saharan Africa. Eur. J. Agron. 155, 127109 (2024).
Google Scholar
Beillouin, D. et al. A global overview of studies about land management, land-use change, and climate change effects on soil organic carbon. Glob. Chang. Biol. 28, 1690–1702 (2022).
Google Scholar
Chivenge, P., Vanlauwe, B. & Six, J. Does the combined application of organic and mineral nutrient sources influence maize productivity? A meta-analysis. Plant Soil 342, 1–30 (2011).
Google Scholar
Laub, M. et al. Combining manure with mineral N fertilizer maintains maize yields: evidence from four long-term experiments in Kenya. Field Crops Res. 291, 108788 (2023).
Google Scholar
Cardinael, R. et al. Sustaining maize yields and soil carbon following land clearing in the forest–savannah transition zone of West Africa: results from a 20-year experiment. Field Crops Res. 275, 108335 (2022).
Google Scholar
Zingore, S., Manyame, C., Nyamugafata, P. & Giller, K. E. Long-term changes in organic matter of woodland soils cleared for arable cropping in Zimbabwe. Eur. J. Soil Sci. 56, 727–736 (2005).
Google Scholar
Vanlauwe, B. et al. Looking back and moving forward: 50 years of soil and soil fertility management research in sub-Saharan Africa. Int. J. Agric. Sustain. 15, 613–631 (2017).
Google Scholar
Chaplot, V. Evidences of plants’ impact on land degradation and climate change: an urgent call for new multidisciplinary research. Geoderma 392, 114984 (2021).
Google Scholar
Silva, J. V. et al. Soil acidity remediation in sub-Saharan Africa requires targeted investments. Nat. Food 6, 799–808 (2025).
Google Scholar
Nelson, P. & Su, N. Soil pH buffering capacity: a descriptive function and its application to some acidic tropical soils. Aust. J. Soil Res. 48, 201–207 (2010).
Google Scholar
Juo, A. S. R., Dabiri, A. & Franzluebbers, K. Acidification of a kaolinitic Alfisol under continuous cropping with nitrogen fertilization in West Africa. Plant Soil 171, 245–253 (1995).
Google Scholar
Hijbeek, R., van Loon, M. P., Ouaret, W., Boekelo, B. & van Ittersum, M. K. Liming agricultural soils in Western Kenya: can long-term economic and environmental benefits pay off short term investments? Agric. Syst. 190, 103095 (2021).
Google Scholar
Moinet, G. Y. K., Hijbeek, R., van Vuuren, D. P. & Giller, K. E. Carbon for soils, not soils for carbon. Glob. Chang. Biol. 29, 2384–2398 (2023).
Google Scholar
Xu, J. M., Tang, C. & Chen, Z. L. The role of plant residues in pH change of acid soils differing in initial pH. Soil Biol. Biochem. 38, 709–719 (2006).
Google Scholar
Gilbert, N. Dirt poor. Nature 483, 525 (2012).
Google Scholar
Jayne, T. S. & Rashid, S. Input subsidy programs in sub-Saharan Africa: a synthesis of recent evidence. Agric. Econ. 44, 547–562 (2013).
Google Scholar
Mapila, M., Njuki, J., Delve, R., Zingore, S. & Matibini, J. Determinants of fertiliser use by smallholder maize farmers in the Chinyanja triangle in Malawi, Mozambique and Zambia. Agrekon 51, 21−41 (2012).
Probert, M. E., Keating, B. A., Thompson, J. P. & Parton, W. J. Modelling water, nitrogen, and crop yield for a long-term fallow management experiment. Aust. J. Exp. Agric. 35, 941–950 (1995).
Bonilla-Cedrez, C., Chamberlin, J. & Hijmans, R. J. Fertilizer and grain prices constrain food production in sub-Saharan Africa. Nat. Food 2, 766–772 (2021).
Google Scholar
Abdulai, A., Owusu, V. & Goetz, R. Land tenure differences and investment in land improvement measures: theoretical and empirical analyses. J. Dev. Econ. 96, 66–78 (2011).
Google Scholar
Zeng, D. et al. Land ownership and technology adoption revisited: Improved maize varieties in Ethiopia. Land Use Policy 72, 270–279 (2018).
Google Scholar
Quisumbing, A. R. & Pandolfelli, L. Promising approaches to address the needs of poor female farmers: resources, constraints, and interventions. World Dev. 38, 581–592 (2010).
Google Scholar
Shepherd, K. et al. Virtual agronomist—an AI-assisted Chatbot for guiding crop management decisions of smallholder farmers in Africa. agriRxiv https://doi.org/10.31220/agriRxiv.2025.00332 (2025).
World Bank. World Development Report 2008: Agriculture for Development. (World Bank, 2007).
FAOSTAT (https://www.fao.org/faostat/).
Ludemann, C. I. et al. A global FAOSTAT reference database of cropland nutrient budgets and nutrient use efficiency (1961–2020): nitrogen, phosphorus and potassium. Earth Syst. Sci. Data 16, 524–541 (2024).
Google Scholar
Soussana, J. F. et al. Matching policy and science: Rationale for the ‘4 per 1000 – soils for food security and climate’ initiative. Soil Tillage Res. 188, 3–15 (2019).
Google Scholar
Dixon, J., Gulliver, A. & Gibbon, D. Farming Systems and Poverty: Improving Farmers’ Livelihoods in a Changing World. (FAO & World Bank, Rome, Italy & Washington, DC, USA, 2001).
International Food Policy Research Institute (IFPRI), 2020, “Spatially-Disaggregated Crop Production Statistics Data in Africa South of the Sahara for 2017”, Harvard Dataverse, V3.
International Food Policy Research Institute (IFPRI), 2024, “Global Spatially-Disaggregated Crop Production Statistics Data for 2020 Version 2.0”, Harvard Dataverse, V4.
Acknowledgements
Much of the work on ISFM and soil health of B.V. and other authors has been supported by various grants of the Bill & Melinda Gates Foundation, recently renamed as the Gates Foundation. The research of J.S. on ISFM in SSA has been supported by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (grants 172940 and 10001421). None of the authors received specific funding for developing the current paper.
Author information
Authors and Affiliations
Contributions
B.V. led the overall development of the paper. K.E.G., J.S. and P.B., R.M., M.C., M.K. and S.Z. respectively led the development of the `Introduction’, `Conceptualization of soil health’, `Conceptual framework linking fertilizer use to soil health’,`Fertilizer use and its impact on crop production and soil health’, and `Economic realities’ sections, respectively. T.A., P.B., R.C., G.F., A.C., A.D., O.A.F., R.H., Z.S., M.K. and M.V.I. contributed to specific sections and reviewed various versions of the paper. All authors have read and approved the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests. Author Tihalun Amede, Associate Editor of npj Sustainable Agriculture, was not involved in the journal’s review of, or decisions related to, this manuscript.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary information (download PDF )
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Reprints and permissions
About this article
Cite this article
Vanlauwe, B., Amede, T., Bindraban, P. et al. Fertilizer and soil health for sustained crop production in sub-Saharan Africa: Theory and conceptual framework.
npj Sustain. Agric. 4, 56 (2026). https://doi.org/10.1038/s44264-026-00161-w
Received:
Accepted:
Published:
Version of record:
DOI: https://doi.org/10.1038/s44264-026-00161-w
Source: Ecology - nature.com
