This study proposes a multi-objective approach for the optimal design of a sustainable Integrated Biodiesel/Diesel Supply Chain (IBDSC) based on first- (sunflower and rapeseed) and second-generation (waste cooking oil and animal fat) feedstocks with solid waste use. It includes mixed-integer linear programming (MILP) models of the economic, environmental and social impact of IBDSC, and respective criteria defined in terms of costs. The purpose is to obtain the optimal number, sizes and locations of bio-refineries and solid waste plants; the areas and amounts of feedstocks needed for biodiesel production; and the transportation mode. The approach is applied on a real case study in which the territory of Bulgaria with its 27 districts is considered. Optimization problems are formulated for a 5-year period using either environmental or economic criteria and the remainder are defined as constraints. The obtained results show that in the case of the economic criterion, 14% of the agricultural land should be used for sunflower and 2% for rapeseed cultivation, while for the environmental case, 12% should be used for rapeseed and 3% for sunflower. In this case, the price of biodiesel is 14% higher, and the generated pollutants are 6.6% lower. The optimal transport for both cases is rail.