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A synthesis of available agronomic datasets and peer-reviewed scientific literature was conducted to: (1) assess the status of micronutrients in sub-Saharan Africa (SSA) arable soils, (2) improve the understanding of the relations between soil quality/management and crop nutritional quality and (3) evaluate the potential profitability of application of secondary and micronutrients to key food crops in SSA, namely maize (Zea mays L.), beans (Phaseolus spp. and Vicia faba L.), wheat (Triticum aestivum L.) and rice (Oryza sativa L.). We found that there is evidence of widespread but varying micronutrient deficiencies in SSA arable soils and that simultaneous deficiencies of multiple elements (co-occurrence) are prevalent. Zinc (Zn) predominates the list of micronutrients that are deficient in SSA arable soils. Boron (B), iron (Fe), molybdenum (Mo) and copper (Cu) deficiencies are also common. Micronutrient fertilization/agronomic biofortification increases micronutrient concentrations in edible plant organs, and it was profitable to apply fertilizers containing micronutrient elements in 60-80% of the cases. However, both the plant nutritional quality and profit had large variations. Possible causes of this variation may be differences in crop species and cultivars, fertilizer type and application methods, climate and initial soil conditions, and soil chemistry effects on nutrient availability for crop uptake. Therefore, micronutrient use efficiency can be improved by adapting the rates and types of fertilizers to site-specific soil and management conditions. To make region-wide nutritional changes using agronomic biofortification, major policy interventions are needed.