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This study presents an analytical framework supporting coal regions in a strategy toward the clean energy transition. The proposed approach uses a combination of value chain analysis and energy sector analysis that enables a comprehensive assessment considering local specificities. Its application to a case study of the Slovakian region Upper Nitra demonstrates practical examples of opportunities and challenges. The value chain analysis evaluates the coal mining industry, from coal extraction to electricity generation, in terms of jobs and business that are at risk by the closure of the coal mines. The complementary energy system analysis focuses on diversification of the energy mix, environmental impacts, and feasibility assessment of alternative energy technologies to the coal combusting sources. The results show a net positive cost benefit for all developed scenarios of replacing the local existing coal power plant. Although the installation of a new geothermal plant is estimated to be the most expensive option from our portfolio of scenarios, it presents the highest CO2 reduction in the electricity generation in Slovakia—34% less compare to the system employing the existing power plant. In addition, the development of a new industrial polo around deep geothermal technology can boost the economic activity in the region by attracting investments in companies providing geological exploration services, transferring the local knowledge from the coal mining industry into an emerging sector.