An agent-based modeling framework is developed and employed to replicate the interactions among urban farms. The objectives are to efficiently manage an urban farm’s food, energy, and water resources, decrease food waste, and increase the food availability for the local community. A case study of eleven farms was investigated in Vancouver, Canada to study the linkages between the resources in the urban food, energy, and water nexus. Each urban farm in the simulation belonged to a community microgrid generating electricity from solar and wind. The local farms aimed to provide fresh produce for their respective local communities. However, at some points, they lacked supply, and at other points, there was excess supply, leading to food waste. Food waste can be converted into fertilizers or bioenergy. However, an alternative solution must be employed due to the natural resources required for production, efficiently managing resources, and adhering to sustainability guidelines. In this paper, an optimization framework was integrated within the agent-based model to create a micro supply chain. The supply chain directly linked the producers with the consumers by severing the links involved in a traditional food supply. Each urban farm in the study collaborated to reduce food wastage and meet consumer demands, establishing farmer-to-farmer exchange in transitional agriculture. The optimization-based micro supply chain aimed to minimize costs and meet the equilibrium between food supply and demand. Regular communication between the farms reduced food waste by 96.9% over 16 weeks. As a result, the fresh food availability increased for the local community, as exemplified by the consumer purchases over the same period. Moreover, the simulation results indicated that the renewable energy generation at the community microgrids aided in the generation of 22,774 Mwh from solar and 2568 Mwh from wind. This has the potential to significantly reduce CO2 emissions in areas that heavily rely on non-renewable energy sources.