Most U.S. farms today specialize in either crop or livestock production, failing to harness the potential economic and environmental benefits of integrated crop–livestock systems (ICLS). This specialization is particularly contradictory for organic operations, which aim to promote biodiversity and reduce reliance on outside sources of feed and fertility. This study investigated the challenges and opportunities experienced by farmers interested in integrating crops and livestock on organically managed farms in Iowa, Pennsylvania, and Minnesota. Qualitative methods, including focus groups and interviews, generated four categories of challenges: farming norms, complexity of management, biophysical conditions, and financial costs, and four categories of opportunities: increasing support for ICLS, financial and labor advantages, biophysical improvements, and animal welfare. Discussion of the data analysis demonstrates how most of the challenges of ICLS are mitigated by opportunities. For instance, increasing support for ICLS means there are growing communities of practice in which farmer-to-farmer knowledge exchange and peer support overcome obstacles to success in these systems. Unmitigated challenges that are beyond the control of farmers include regional infrastructure, financing and insurance, and long time horizon for returns. These three unmitigated challenges may require interventions such as policy support, economic incentives and social infrastructure to enable successful farm transitions to ICLS in this region.