In developing countries in Africa, agricultural intensification follows increasing food demand from a growing population. Agricultural intensification, coupled with poor land use policy, is transforming Kenya’s agroecosystems. There is little information on how such intensification has affected the diversity and functioning of Arbuscular Mycorrhizal Fungal (AMF) communities, which are crucial for the maintenance of soil quality (soil structure) and crop performance (nutrient use efficiency). In this study we aim to quantify (i) the effect of management changes (increased tillage, monocropping vs. crop rotations, organic amendments) on AMF communities; (ii) the impact of these AMF community changes on the physical soil structure; and (iii) the interaction between AMF, earthworms and plants with respect to soil structure. The first aim will addressed by field inventarisation of AMF communities in three long"term trials in Kenya. For the second aim, we will trace the dynamics of crop residues (through signatures of 15N and 13C) into glomalin associated with soil aggregates. The third aim will be addressed by measuring plant productivity under combinations of AMF and earthworm species in a greenhouse study. Finally, we will identify optimal sustainable management with respect to plant productivity, AMF and soil macrofauna for the studied systems.