This work focused upon design and operation of biodiesel production facilities in support of the broader goal of developing a strategic approach to the development of biorefineries. Biodiesel production provided an appropriate starting point for these efforts. The work was segregated into two stages. Various feedstocks may be utilized to produce biodiesel, to include virgin vegetable oils and waste cooking oil. With changing prices, supply, and demand of feedstocks, a need exists to consider various feedstock options. The objective of the first stage was to develop a systematic procedure for scheduling and operation of flexible biodiesel plants accommodating a variety of feedstocks. This work employed a holistic approach and combination of process simulation, synthesis, and integration techniques to provide: process simulation of a biodiesel plant for various feedstocks, integration of energy and mass resources, optimization of process design and scheduling, and techno-economic assessment and sensitivity analysis of proposed schemes. An optimization formulation was developed to determine scheduling and operation for various feedstocks and a case study solved to illustrate the merits of the devised procedure. With increasing attention to the environmental impact of discharging greenhouse gases (GHGs), there has been growing public pressure to reduce the carbon footprint associated with fossil fuel use. In this context, one key strategy is substitution of fossil fuels with biofuels such as biodiesel. Design of biodiesel plants has traditionally been conducted based on technical and economic criteria. GHG policies have the potential to significantly alter design of these facilities, selection of feedstocks, and scheduling of multiple feedstocks. The objective of the second stage was to develop a systematic approach to design and scheduling of biodiesel production processes while accounting for the effect of GHG policies. An optimization formulation was developed to maximize profit of the process subject to flowsheet synthesis and performance modeling equations. The carbon footprint is accounted for through a life cycle analysis (LCA). The objective function includes a term reflecting the impact of the LCA of a feedstock and its processing to biodiesel. A multiperiod approach was used and a case study solved with several scenarios of feedstocks and GHG policies.