A quantitative methodology for the assessment of geotopes that can be used for the sustainable management and conservation of the geological heritage of an area is here presented. As sustainable development, education and conservation are core issues for the successful management of any protected area, this study focuses on the development of specific indexes necessary for determining values concerning the tourism, educational and protection requirements of geotopes. The proposed methodology is based on a series of criteria that cover not only the geological and geographical importance of a geotope but also its scientific, ecological, cultural, aesthetic and economic significance. Based on these criteria, the resulting scientific, ecological, cultural, aesthetic, economic and potential for use scores of each geotope are used to estimate, respectively, the touristic, educational and protection-need value indexes for each geotope on a scale ranging from 1 to 10. This methodology was implemented and tested in two areas in the island of Crete, namely the Psiloritis Natural Park, a European and Global geopark, and the Lassithi Mountains, producing reliable results, which are in agreement with the geopark’s activities and values. The proposed quantitative assessment method is, therefore, a useful tool. It serves the requirements for the adequate management and protection of geoheritage within a territory as it can reveal priorities for sustainable tourism development, including geotourism and educational tourism activities and the conservation of geotopes.