European Territorial Cooperation (ETC) programmes are currently concluding the operational cycle 2007-2013. In the Mediterranean area, on-going evaluation processes of sixteen ETC programmes have revealed heterogeneous approaches as well as little interest to assess existing complementarities with other neighbour ETC programmes. European Union (EU) regulation for the programming period 2014-2020 integrates innovations in the evaluation process by requesting ‘evaluation plans’ and encourages effective synergies between programmes. Accordingly, this paper identifies a cooperation framework for developing cross-programme exercises of evaluation in the Mediterranean area and proposes a methodology of joint programme thematic evaluation in the domain of renewable energy.