This research deals with the evaluation of tourist attractions in selected protected areas (PAs) in Serbia for the purpose of developing ecotourism. Using the integral AHP-SWOT method, two authentic mountain areas were analyzed—Stara Planina Nature Park and Suva Planina Special Nature Reserve. The results confirmed the presence of numerous natural and, to a lesser extent, anthropogenic resources that represent the basis for the future ecotourism activities. However, significant weaknesses were also registered, which are reflected in overall poverty, underdeveloped infrastructure and depopulation. The analysis also showed that the highest rated factors for the development of ecotourism are local products that should be offered on the regional market, as well as the use of the geographical position of both areas (near the state border) through the use of donor funds (IPA funds). The application of the AHP-SWOT method enabled the definition and prioritization of several development strategies, of which the ones with the greatest weight are based on the use of the variegated biodiversity of both PAs. This research advances knowledge about strategic decision-making in PAs and could be beneficial to destination managers for the creation of successful strategic plans. Results suggest that future actions should be aimed at maximizing the detected advantages, which means creating an appropriate development policy, drafting legislation, encouraging social mobilization activities and determining the institutional elements for the development and management of ecotourism.