Water and nutrient stress are major constraints to agricultural production in East and West Africa. A better understanding of the impact of soil fertility management on the interactions between soil organic matter (SOM), soil structure, and nutrient and water use efficiency is pivotal to the optimal exploitation of scarcely available organic resources and the design of sustainable cropping systems. Although different functional groups of soil macrofauna greatly affect soil structure, SOM, soil water and nutrient dynamics, quantitative understanding and optimization of their role is lacking. Our research programme comprises an interdisciplinary approach to investigate the effects of agricultural management on soil quality and nitrogen- and water use efficiency, emphasizing the role of soil macrofauna biodiversity across soil types and climates in East and West Africa.