Predominant forms of food and energy systems pose multiple challenges to the environment as current configurations tend to be structured around centralized one-way through-put of materials and energy. In addition, these configurations can introduce vulnerability to input material price and supply shocks as well as contribute to localized food insecurity and lost opportunities for less environmentally harmful forms of local economic development. One proposed form of system transformation involves locally integrating “unclosed” material and energy loops from food and energy systems. Such systems, which have been termed integrated food-energy systems (IFES), have existed in diverse niche forms but have not been systematically studied with respect to technological, governance, and environmental differences. As a first step in this process, we have constructed a taxonomy of IFES archetypes by using exploratory data analysis on a collection of IFES cases. We find that IFES may be classified hierarchically first by their primary purpose—food or energy production—and subsequently by degree and direction of vertical supply chain coordination. We then use this taxonomy to delineate potential governance challenges and pose a research agenda aimed at understanding what role IFES may play in food and energy system transformation and ultimately what policies may encourage IFES adoption.