Industrial energy efficiency measures are proving financially viable, but the implementation rate is stagnating. This results in the need to develop a comprehensive and standardized methodology to assess the multiple benefits of energy efficiency measures in an industrial context. However, a comprehensive methodology to assess the multiple benefits of energy efficiency measures are omitted. The methodology, as presented in this study, was developed and validated based on nine case studies performed between 2016 and 2018 in the Swiss industrial sector. The aim is to close this gap with the introduction of a three-phase standard methodology, applicable to a wide range of industrial processes and energy efficiency measures. The three phases are further split into individual steps, each pursuing a specific goal in order to facilitate the implementation of energy efficiency measures. The first phase, the delimitation, aims at defining the system boundaries of the considered industrial process(es). The second phase, the assessment, involves the identification, the quantification, and the monetization of multiple benefits, as well as the qualitative assessment of non-monetizable multiple benefits. The last phase, the evaluation, focusses on the integration of the obtained results into the financial valuation of the energy efficiency measure and, therefore, on the cash flow analysis and the determination of the payback time under consideration of the monetizable multiple benefits. The study has shown that the consideration of monetizable multiple benefits may reduce the payback time of energy efficiency measures by up to 40-85%.