Protected areas are prime areas for ecotourism development, attracting large numbers of visitors to an abundance of ecologically significant and often sensitive flora and fauna. The current study identified adverse impacts of ecotourism in four prominent tourist hotspots in Iran, namely Lar National Park, Jajrud Protected Area with Sustainable Use of Natural Resources, Tangeh Vashi National Natural Monument, and Kavdeh Wildlife Refuge. Impacts were compared against the IUCN guidelines according to the degree of ecological sensitivity and multiple managerial objectives. In addition, an analytic network process (ANP) was applied within a Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis to identify optimal strategies for reducing threats and weaknesses and improving opportunities and strengths for sustainable ecotourism management. We found the greatest negative impacts of ecotourism in a Jajrud that was exposed to rapidly expanding urbanisation and the corresponding development of economic and physical activities. Conversely, the least negative impact occurred in a national park (Lar) that was managed based on conservation approaches, accounting for high ecological sensitivities, and adapting legal prohibitions. The SWOT-ANP analysis demonstrates that certain strategies can minimise impacts and should be adopted as conservation tools by protected area managers and land planners.