Aims Despite the importance of the soil microbiota to plant growth, the role of soil microorganisms in crop-weed competition remains largely unexplored. Here, we investigated the influence of soil microbial communities and weed species on the outcome of maize-weed interactions. Methods The relationships between soil bacterial and fungal communities and plant growth under different cultivation managements (plant monocultures and coexistence between Bidens pilosa L. and Amaranthus viridis L. and maize) and soil conditions (sterilized soil and sterilized soil with microbiota reconstitution) were studied. Plant dry matter and soil microbial diversity were analyzed after 43 days of cultivation. Results Maize grew better in the presence of the weeds, indicating the occurrence of facilitation under the cultivation conditions tested. Plant cultivation led to different soil microbial communities after soil sterilization and microbiota reconstitution. In sterilized soil, the colonizing microbiota led to higher maize growth in the presence of B. pilosa . The opposite was observed in the soils with microbiota reconstitution, where maize grew better with A. viridis . Conclusions Soil microbial communities are involved in the facilitation of maize growth by B. pilosa and A. viridis . Facilitation intensity depends on the weed species and the way coexisting plants shape the soil microbial communities.