Beneficial soil microbiota especially arbuscular mycorrhizal fungi (AMF) deliver essential agroecosystem services in organic farming systems, where the application externalities is often limited. Undoubtedly, organic farming provides optimal conditions for agroecological functioning due to minimal soil disturbance and limited use of agrochemicals. In this context, beneficial soil microbiota are expected to deliver optimal ecosystem services. Nevertheless, the composition, diversity and function of beneficial rhizospheric microorganisms including AMF communities vary upon agronomic practices and soil conditions. Moreover, it is well known that some modern crop cultivars are less responsive to AMF, since they are bred for high intensive agricultural systems where there is sufficient supply of nutrients especially P. Until now, the establishment and function of AMF in organic cropping systems is still poorly understood. Such information is a prerequisite for the implementation of efficient cropping systems that capitalize on biological processes, a key step towards agricultural sustainability. The overall aim of this review is to provide insights on increasing mycorrhizal symbiosis and crop productivity in organic agroecosystems through innovative, temporal and spatial manipulation of species and genetic diversity at the crop cultivar, AMF species and cover crop management levels. The bulk of this review underscores the importance of examing different levels of diversification in organic farming systems, considering functional identity (single species), composition (mixed species) and diversity (heterogeneity within species) and how such components contribute to delivery of multiple agroecosystem services.