The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no‐till, had a much greater impact on nearly everything measured compared to the crop planted. No‐till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no‐till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff—both of which have ecosystem‐level effects and both direct and indirect effects on humans and other organisms. Microbial communities are essential for nutrient cycling in ecosystems. Disturbance, such as tilling, alters the composition of microbial communities in corn and soy agroecosystems. The changes in these communities affect their composition and function, thus changing the ecosystem services they perform, such as cycling nitrogen.