Cities have emerged to become a major challenge and at the same time can evolve to an instrument for supporting the global sustainability efforts. Cities consume 78% of the world’s energy and produce more than 60% of greenhouse gas emissions and 70% of global waste. In the Mediterranean region, two thirds of the population live in urban areas and urban population it is expected to increase to about 170 million in the countries on the northern shore and to over 300 million to the south and east by 2050. Thus, urban sustainability has become increasingly mainstream in policymaking towards a competitive, secure and decarbonized built environment. In order to promote sustainability efforts, local governments must have the capacity to measure it. Various sustainability methodologies and rating systems have been developed including different performance indicators, like the energy use intensity, carbon emissions, smart readiness, potable water consumption and recycled materials. However, most of them are following a building scale approach, which does not fully exploit the potential for synergies that groups of buildings might offer. The Sustainable MED Cities project, is an on-going effort aiming to provide an easy to use, harmonized methodology and an open-source software to support the assessment, planning and overall and monitoring effective measures to improve sustainability of the built environment at city scale. The work is a collaborative work in the Mediterranean basin among Greece, Italy, Jordan, Lebanon, Spain, and Tunisia and capitalizes CESBAMED, an existing transnational methodology and assessment tool for buildings and neighbourhoods in European Mediterranean countries. This work reviews the common method and tools for the assessment and the final sustainability rating score. Emphasis is given on the proposed key performance indicators that cover all fields of sustainability, at building, neighbourhood and city scale.