Despite being generally accepted as a promising conservation practice to reduce nitrate pollution and promote soil sustainability, cover crop adoption in Midwestern U.S. agriculture is low. Based on focus groups, surveys, and partial budgets, we calculated the annual net returns to cover crop use for farmers in Illinois, Iowa, and Minnesota; and elicited farmers’ perceptions about the pros and cons of incorporating cover crops to their row cropping systems. The novelty of our methodology resides in comparing each farmer’s practices in the portion of their cropping system with cover crops (typically small), against their practices in the other portion of their cropping system without cover crops. The resulting comparisons, accounting for farmer heterogeneity, are more robust than the typical effects calculated by comparing indicators across cover crop users and unrelated non-adopters. Our results highlight the complicated nature of integrating cover crops into the crop production system, and show that cover crops affect whole farm profitability through several channels besides establishment and termination costs. Despite farmers’ positive perceptions about cover crops and the availability of cost-share programs, calculated annual net returns to cover crops use were negative for most participants.