Biogas plants experience changes in biogas production due to seasonal weather changes, waste composition variation, operating methods, and other factors. These natural changes affect the economics of the subsystems. Generally, profit can be produced by selling the raw gas or the purified biomethane to the local gas distribution network, or by selling generated electricity in a dedicated power plant. Biogas plants are basically designed for sewage treatment and processing food waste produced from nearby urban areas. In this study, we analyzed the thermoeconomics of a biogas-fueled micro-gas turbine (MGT) system, which is coupled with a bottoming organic Rankine cycle (ORC) for a target biogas plant in Busan, Republic of Korea. Both systems were designed for heating a biodigester using heat in the exhaust gas. For the MGT, we considered a series of commercial multi-unit systems, and the partial-load performance was derived from the performance curves. For the ORC, we first designed an exergy-optimized cycle using n-pentane, a widely used working fluid, and then the partial-load performance was analyzed. The economic parameters were expressed based on the system size. We analyzed the system economics based on the annual utilization ratio (the produced power to the available maximum power) and the net present value (NPV). The effect of system control, methane concentration, and overhaul periods were analyzed. A membrane biogas upgrade system is considered for the comparison. In particular, we have found the followings: first, the biogas power generation systems showed the optimal system scales to provide the maximum NPVs according to the seasonal changes; second, the economics of the system were very sensitive to changes in the biogas methane ratio, electricity prices and overhaul periods; and third, in Korea, where electricity prices are low and natural gas prices are high, the competitiveness of power generation system is very low compared to a system that sells biogas directly.