In a variety of ecosystems, interactions between soil microbiota and weedy plants can strongly affect population and community dynamics of these plants. However, weed–soil microbe interactions are not well characterized in field-crop agroecosystems. In Minnesota (USA), we repeatedly applied a fungicide (benomyl) to field plots in a corn–soybean crop rotation in each of 3 years, and sowed experimental weed communities containing host species for arbuscular-mycorrhizal fungi (AMF) and non-host species. Benomyl typically suppresses formation of mycorrhizal symbiosis in AMF-host plant species, and may also affect other soil fungi. We assessed weed density and biomass production, and monitored AMF colonization rates in each of 3 years. We found that weed density, biomass, community composition and the relative performance of AMF-host and non-host weed species were all significantly responsive to fungicide applications, although for all attributes responsiveness was variable. Fungicide application increased total weed density and biomass production in nearly all cases; most effects were modest but reached a maximum of 49%. Fungicide application also increased the relative performance of non-host species in most cases, although most effects were again modest. Our findings are the first assessment of responses by field-crop weeds to direct manipulation of soil microbial communities in a field setting, and suggest that the population and community ecology of these weeds can be strongly affected by the fungal component of soil microbiota.