Abstract Environmental performance evaluation (EPE) brings benefits to organizations, if they are interested in improvement and demonstration of their environmental performance. Environmental performance evaluation is an environmental management tool which is standardized by STN EN ISO 14031 and provides quantified data about environmental performance of the organizations. It is possible to ensure a condition for registration according to EMAS by application of environmental performance evaluation. The methodology formation of Environmental performance evaluation process, areas of using environmental indicators, which are important elements in planning of this process and benefits from application of EPE in organizations are described in this paper. The aim of the experimental part was to describe and analyze this process in model organization, which have established environmental management system and propose some improvements of its EPE. Presented proposals are related to implementation of management performance indicators to environmental performance evaluation of the organization and relative operational performance indicators elimination because of results distortion possibility in trend evaluation.