The need for integrated methodological framework for sustainability assessment has been widely discussed and is urgent due to increasingly complex environmental system problems. These problems have impacts on ecosystems and human well-being which represent a threat to economic performance of countries and corporations. Integrated assessment crosses issues; spans spatial and temporal scales; looks forward and backward; and incorporates multi-stakeholder inputs. This study aims to develop an integrated methodology by capitalizing the complementary strengths of different methods used by industrial ecologists and biophysical economists. The computational methodology proposed here is systems perspective, integrative, and holistic approach for sustainability assessment which attempts to link basic science and technology to policy formulation. The framework adopts life cycle thinking methods—LCA, LCC, and SLCA; stakeholders analysis supported by multi-criteria decision analysis (MCDA); and dynamic system modelling. Following Pareto principle, the critical sustainability criteria, indicators and metrics (i.e., hotspots) can be identified and further modelled using system dynamics or agent based modelling and improved by data envelopment analysis (DEA) and sustainability network theory (SNT). The framework is being applied to development of biofuel supply chain networks. The framework can provide new ways of integrating knowledge across the divides between social and natural sciences as well as between critical and problem-solving research.