Small grains provide agronomic benefits that are critical to the success of organic production, and opportunities within local food movements create expanded markets for small grains. However, diversifying rotations with small grains can present challenges related to production, infrastructure, and markets. Here, we draw upon over two decades of integrated research and Extension efforts to support organic small grain production in the Upper Midwest, Northeast, and other regions of the United States where these crops are underutilized. Lessons learned have led to the development of guiding principles for a systems‐level approach to support regional organic small grain production. Forming innovative partnerships between farmers, researchers, and end users is critical. This enables research, production, and markets to adjust to local needs, adapt to available infrastructure, and foster local grain economies. The key research challenges that lie ahead are also discussed, especially adapting organic grain production practices to regional conditions and changing climates. The systems‐level approach to organic small grain research highlighted here will increase the success and resilience of organic farms across the United States and expand the adoption of organic small grain production.