Striving towards a resource efficient society requires an adjustment of energy systems towards renewable options. It is also of high importance to make use of products and materials to a higher degree. Biogas production has the potential to recover nutrients and energy from organic by-products, as well as to substitute fossil fuels in the energy system. Resource efficiency relates to the economic, energy and environmental performance of the system studied. A comprehensive research design for assessment of the resource efficiency of biogas production systems is described in this paper. The research design includes the following parts: identification of cases, defining scenarios, system development, evaluation perspectives and systems analysis. The analysis is performed from three perspectives; economy, energy and environment.