Food supply chains (FSC) have been receiving increased attention throughout the recent years. The inherent products’ characteristics associated with the logistics activities require an approach beyond the traditional one, where specific food supply chain characteristics need to be considered namely customer perception of freshness, which appears as an intangible value but with a high impact in sales, as well as environmental aspects associated with these systems. This work propose a comprehensive approach for design and planning of a food supply chains, where supply chain lead times are explored while being integrated with transportation mode selection, environmental impacts, and demand uncertainty. A multi-objective approach is developed considering the maximization of an economic indicator, and the minimization of environmental impacts as well as FSC lead time. An example is used to show the methodology application.