Despite common acknowledgement of the value of protected areas as instruments in ensuring sustainability, and their promotion for the achievement of policies on halting the loss of biodiversity, there is no common approach today for monitoring and evaluating them. This paper presents a novel integrated nature conservation management procedure developed to monitor and evaluate the sustainability of Mediterranean protected areas. This procedure was successfully implemented and formally evaluated by protected area managers in six Mediterranean countries, results of which are presented here together with an overview of the web-based Decision Support System (DSS) developed to facilitate its wide adoption. The DSS and procedure has been designed and evaluated by managers as a useful tool, which facilitates and provides needed procedural guidance for protected area monitoring whilst minimizing input requirements to do so. The procedure and DSS were developed following a review of existing protected area assessment tools and a detailed primary investigation of the needs and capacity of its intended users. Essentially, the procedure and DSS guides provide the facilities for protected area managers, in following a participatory approach to develop a context-specific sustainability monitoring strategy, for their protected area. Consequently, the procedure is, by design, participatory, context specific, holistic and relevant to protected area management and institutional procedures. The procedure was piloted and formally evaluated in Greece, Italy, Turkey, Egypt, Malta and Cyprus. Feedback collected from the pilot evaluations is also summarised herein.