Purpose: Push-pull is an intercropping technology that rapidly spreads among Sub-Saharan smallholder farmers. It intercrops maize with Desmodium to fight off stem borers, eliminate parasitic weeds, and improve soil fertility and yields. The above-ground components of push-pull cropping have been well investigated. However, impact on and from the soil microbiome and its role in diverse ecosystem benefits are unknown. Here we describe the soil microbiome associated with push-pull and compare it with maize monoculture.Methods: Soil samples from long-term maize-desmodium intercropping and maize monoculture plots were analysed using 16S and ITS metagenomics.Results: Maize-desmodium intercropping caused a strong divergence in fungal microbiome, which was more diverse and species rich than monoculture plots. Zooming into genera revealed that intercropping enhanced fungal genera linked to important ecosystem services. These include mycorrhizal and endophytic groups such as Edenia, Acrocalyma and Colletotrichum, saprophytic and decomposer fungi like Pithya and Cristinia and fungi with biocontrol properties, for instance, Talaromyces, Penicillin, Clonostachys and Trichoderma. Fungal genera enriched in monoculture plots were few, and were functionally linked to plant diseases (for example Didymella, Curvularia and Parastagonospora), and human pathogenic taxa (Exserohilum, Curvularia and Aspergillus). Although separating well, bacterial microbiomes did not, except in a few genera, differ between treatments. Conclusion: Maize-desmodium intercropping diversifies fungal microbiomes and favors taxa that are associated with important ecosystem services, including plant health, productivity and food safety. Further studies should increase the resolution of shifts noted above, experimentally ascertain the inferred functions, and translate this knowledge to improve cropping systems.