A resilient and sustainable way of life presupposes the reduction of the energy consumption and the relevant greenhouse gas (carbon) emissions. This approach leads to the establishment and implementation of various directives and regulations regarding the refurbishment of the existing building stock. Often, these regulations exclude heritage buildings due to the lack of robust methodologies which will ensure a balance between the energy retrofitting and preservation of the building’s heritage values. Heritage buildings however, host a variety of public uses and their holistic and successful energy upgrade could serve as an excellent example of a heritage building energy refurbishment to the community. Thus, there is an emerging need for developing such methodologies. This paper aims to propose an integrated methodology for the energy retrofitting of heritage buildings, based on a multi-criteria decision-making process for the selection of the appropriate retrofitting solutions considering simultaneously the heritage significance, the heritage and the energy impact.