Abstract Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants, including many important agricultural crops. These fungi facilitate plant nutrient uptake, promote soil aggregation and use a significant portion of reduced carbon from the plants. AMF functional traits differ considerably among and within species, meaning that functional properties of a mycorrhizal community depend on its composition. Here we review studies exploring the effects of agricultural practices such as tillage, crop rotation, fertilization, pesticide application, irrigation and grazing on AMF communities. Although it is difficult to generalize the results of studies performed under different soil and climatic conditions, some universal patterns emerge. For example, soil tillage reduces the abundance of Scutellospora spp.; phosphorus fertilization lowers the extent of AMF root colonization; and diversification of crops results in more diverse AMF communities. We now need to design simple and reliable field tests for quantifying the effects of AMF communities on crop growth, yields and sustainability of the agro-ecosystems.