Improving the regional organization of food flow requires an understanding of system constraints. System transformation is necessary if the system is to include regional, independent wholesale food suppliers and to distribute food in an equitable and sustainable manner. Regional suppliers play a pivotal role in overall food system resilience, an emerging issue in wake of the numerous failures in conventional food supply chains exacerbated by COVID-19-related disruptions. Yet alternative supply chains that link local producers with towns and urban centers regionally, represent a small fraction of our nation's food suppliers. They struggle to compete with larger distribution networks that can supply products in-and out-of-season by global procurement. The upper Midwest harbors numerous local and regional food supply chains consisting of farms, processors, trucking companies, wholesalers and other firms that share a commitment to sustainability and local economic development. A constellation of challenges hamper their emergence, however, even as larger scale food supply chains flounder or fail to effectively serve communities. Informed by Donella Meadows's work on leverage points for systemic change, a collaborative, transdisciplinary and systems research effort examined conventional food supply networks and identified key opportunities for shifting food supply chain relationships. System concepts such as stock and flow, leverage points, and critical thresholds helped us to frame and identify challenges and opportunities in the current system. The second and third phase of our collaborative research effort occurred over 4 years (2013–2016) and involved twenty-six people in co-generation of knowledge as a loose-knit team. The team included farmers, supply chain practitioners, students, academic staff and faculty from multiple departments and colleges. Our primary method was to host public workshops with practitioner speakers and participants to identify dominant narratives and key concepts within discourses of different participants in distribution networks. The literature review was iterative, based on challenges, ideas and specific questions discussed at workshops. Our research exposed two meta-narratives shaping the supply chain: diversity and efficiency. In addition to these high-leverage narratives, we identified and examined five key operational thresholds in the Upper Midwest regional food system that could be leveraged to improve food flow in the region. Attention to these areas makes it possible for businesses to operate within environmental limits and develop social structures that can meet scale efficiencies necessary for economic success. We iteratively shared this co-produced knowledge with decision-makers via local food policy councils, local government, and national policy circles with the goal of supplying actionable information. This phased action research project created the environment necessary for a group of food system entrepreneurs to emerge and collaborate, poised to improve system resilience in anticipation of food system disruptions. It forms the basis for on-going research on food flow, regional resilience, and supply chain policy.