The environmental performance has been gaining place in the decision makers board of organizations. Higher Education Institution with environmental awareness required, as all organizations, tools to help the development of policies and programs toward a better performance. Key Performance Indicators are usually part of economic and financial decision-maker boards. The definition of a set of Key Performance Indicators regarding the relevant environmental aspects of an institution seems to be a step toward the integration of environmental issues in the overall management. In this paper, a methodological proposal to define environmental Key Performance Indicators for Higher Education Institutions with robust Environmental Management System (ISO certified or EMAS verified) is proposed together with a validation system based on Metaperformance evaluation indicators. The proposal is based on the significant environmental aspects along with the degree of operational control that the organization has over them. Additionally, a list of over 140 environmental indicators described and classified are offer as inspiration. An environmental unit, EPSA, of Universitat Politècnica de València, EMAS verified, is used as a pilot case study. As a result, seven Key Performance Indicators are defined, although only three could be fully assessed. Energy consumption, waste management treatment and greenhouse gases emissions are the key elements of these indicators. Institutions with robust Environmental Management Systems have significant advantages on the identification of the relevant environmental aspects and the definition of the goals that set the start point to define Key Performance Indicators. However, these systems do not ensure the availability of data or the quality desired. In the case study, additional resources are required in order to obtained results for the Key Performance Indicators that assess it significant environmental aspects. The effort would benefit both the Environmental Management System and the decision-making board.