Core Ideas Swine manure enriched the soil food web in ways that conventional fertilizers did not. Tillage increased abundances of enrichment‐opportunist nematodes. Aldicarb nematicide negatively affected nontarget free‐living nematodes, but inconsistently. Corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] are important crops and a major part of the US landscape. Soybean and corn production practices influence soil ecology, and good soil quality is essential for crop productivity. Fertilizer application, tillage, and pesticide application are foundational practices in these crops, and the nematode community is a useful indicator of changes in soil ecology. Therefore, the nematode community was assessed in a series of 2‐yr experiments in corn and soybean production. Long‐term conventional tillage and minimum tillage treatments were in place at the study site for 14 yr at the start of the study. Additional treatments were combinations of conventional fertilizers (N‐P‐K and N‐P‐K‐S), liquid swine manure, and granular nematicide (aldicarb or terbufos). Manure application consistently and substantially increased bacterivore abundances compared with conventional fertilizers or untreated control, with effects continuing over a year after application. Bacterivores are resource opportunists, so this indicates that manure application enriched the soil food web in ways that conventional fertilizers did not. Tillage also enriched the soil food web, based on increased bacterivore and fungivore abundances, albeit inconsistently between rotations. Aldicarb nematicide was generally effective against plant‐parasitic nematodes but also decreased abundances of nontarget free‐living nematodes, albeit inconsistently. Omnivores and predators had relatively small abundances throughout the study, and neither tillage nor fertilizer application affected these nematodes. In summary, agricultural practices influenced soil ecology, and manure application had the strongest influence among the practices tested, shifting the food web to an enriched condition.