Flex Fuel Polygeneration (FFPG) is the use of multiple primary energy sources for the production of multiple energy carriers to achieve increased market opportunities. FFPG allows for adjustments in energy supply to meet market fluctuations and increase resiliency to contingencies such as weather disruptions, technological changes, and variations in supply of energy resources. In this study a FFPG plant is examined that uses a combination of the primary energy sources natural gas and renewable natural gas (RNG) derived from MSW and livestock manure and converts them into energy carriers of electricity and fuels through anaerobic digestion (AD), Fischer-Tropsch synthesis (FTS), and gas turbine cycles. Previous techno-economic analyses of conventional energy production plants are combined to obtain equipment and operating costs, and then the 20-year NPVs of the FFPG plant designs are evaluated by static and stochastic simulations. The effects of changing operating parameters are investigated, as well as the number of anaerobic digestion plants on the 20-year NPV of the FTS and FFPG systems.