This chapter outlines the connection between human nutrition and soil health, and describes practical technologies that can regenerate the soil while producing nutritious plant and animal-based food in Sub-Saharan Africa. It explains how improving soil management can lead to improved production of nutritious food as well as improvement of the human gut microbiome, both of which are vital for our health and well-being. The chapter begins with an overview of the Sub-Sahara African food system context, looking at soil conditions and land degradation as well as the food security and nutrition situation. The chapter continues with a discussion of the services provided by the soil ecosystem. It explores the connections between the microbiome of the soil, plants and the human gut and changes that have occurred in the human gut because of diet changes and environmental factors. This is followed by a description of the impacts of agriculture on soils and human health and a discussion of the benefits of cultivating soil microbial communities. The final section explores some principles and practices of the agroecology approach that can be applied in Sub-Saharan Africa to improve soil health, food security and nutrition. It describes various crop and livestock production methods that have been successfully implemented in African contexts. To develop more sustainable food systems and address the malnutrition problems facing the continent, it is vital that development agents embark on a continent-wide effort to improve soils using agroecological methods.