Nature provides life-support services which do not merely constitute the basis for ecosystem integrity but also benefit human societies. The importance of such multiple outputs is often ignored or underestimated in environmental planning and decision making. The economic valuation of ecosystem functions or services has been widely used to make these benefits economically visible and thus address this deficiency. Alternatively, the relative importance of the components of ecosystem value can be identified and compared by means of multi-criteria evaluation. Hereupon, this article proposes a conceptual framework that couples ecosystem function analysis, multi criteria evaluation and social research methodologies for introducing an ecosystem function-based planning and management approach. The framework consists of five steps providing the structure of a participative decision making process which is then tested and ratified, by applying the discrete multi-criteria method NAIADE, in the Kalloni Natura 2000 site, on Lesbos, Greece. Three scenarios were developed and evaluated with regard to their impacts on the different types of ecosystem functions and the social actors' value judgements. A conflict analysis permitted the better elaboration of the different views, outlining the coalitions formed in the local community and shaping the way towards reaching a consensus.