In this paper, a decision-making approach based on the triple bottom line concept is presented for evaluating the sustainability of demand-oriented biogas supply (DOBS) programs with regard to their environmental, economic, and social impacts. For the assessment, an indicator system was developed, whose main parameters were quantified by integrating emergy analysis, economic benefit assessment, and a proposed social risk accounting method. The Charnes-Cooper-Wei-Huang (CCWH) model with constrained cone was adopted to calculate the comprehensive sustainability via the synthesis of the economic, environmental, and social indicators, in which eight scenarios were set according to the flexibility hierarchy of biogas supplied for load demand, biogas production mode, and feeding substrates. The evaluation results show that the DOBS scenario of supplying for real-time varying power demand by using straw and livestock manure has the highest sustainability score in our case study. Based on the results, corresponding managerial implications are proposed.