Industrial wind farms are being developed within many protected areas, such as in EU Natura 2000 sites; this includes proposals on small Mediterranean islands, such as Samothraki in Greece. Scarce wild land areas on islands may be particularly vulnerable to landscape-scale degradation; this may have serious negative societal impacts. Samothraki’s resident perceptions were surveyed in the wake of such a proposal, in June 2018. Of 98 respondents, 48% reported they were against the wind farm plan, while 22% did not take sides. We compare for-and-against sub-group perceptions of the proposed wind farm with potential impacts on the landscape and explore residents’ opinions on ecosystem services and environmental pressures and threats. Conflict over the wind farm was prevalent; residents most frequently reported that the proposal threatens aesthetic and landscape qualities. Aesthetic qualities were also the second highest ranked ecosystem services, after freshwater provision. However, other threats, such as livestock overgrazing, top residents’ opinion of major environmental problems on the island. The questionnaire survey used provides a scoping assessment, which may assist in identifying “conflict hotspots” for wind farm development. A critical review of wind farm planning in protected areas is presented in light of insights gained from this survey and other relevant studies.