Ecotourism in protected areas facilitates responsible travel to natural places that conserve the environment, deliver economic benefits to local communities, and offer interpretation and education to visitors. Proper planning and sufficient monitoring of ecotourism sustainability indicators is needed to manage visitor activities in protected areas. Therefore, identifying the major impacts and mitigating them in the early stages of ecotourism development could contribute significantly to the achievement of sustainable development. There is a current gap between the situation in the field and academic contributions to this problem in protected areas of Iran. In the present study, we evaluated ecotourism sustainability levels in four different types of protected areas in Iran, including Lar National Park, Jajrud Protected Area with Sustainable Use of Natural Resource Areas, Tangeh Vashi National Natural Monument, and Kavdeh Wildlife Refuge. We developed a comprehensive list of ecotourism sustainability indicators, including 38 indicators in the environmental–physical dimension, 42 indicators in the demographic–social dimension, and 30 indicators in the economic–institutional dimension. Harnessing local community expertise, we adopted a Delphi approach to determine sustainability levels and factors impacting sustainability. Ecotourism in Lar National Park was most sustainable because of the high levels of restrictions protecting the area and the difficulty in access. Conversely, ecotourism sustainability was lowest at Tangeh Vashi National Natural Monument, which allowed for an uncontrolled influx of visitors. We discuss further factors that impact sustainability, such as population growth, expanding urbanization, an increase in physical and economic activities, and extended annual periods of ecotourism activities. Although the presented ecotourism sustainability indicators are specific to Iran, this study can also be seen to provide a template to plan for sustainable ecotourism in other countries. Altogether, our results suggest conducting a type-by-type analysis of the particular circumstances of various protected areas.