Alpine protected areas provide a wide range of ecosystem services, with climate regulation being one of the most significant. In line with the European Biodiversity Strategy for 2030, which emphasizes the conservation and enhancement of ecosystem services, there is an urgent need to correctly manage these areas in order to maximize biodiversity conservation and the supply of ecosystem services. To achieve efficient management and decision-making processes, it is crucial to first assess the current supply of ecosystem services and to have a basic reference for monitoring activities. Various approaches can be used to evaluate the carbon storage, a widely used indicator of the climate regulation service. In this study three approaches were compared: fieldwork data collection, the Italian National Inventory and the TESSA toolkit. Discrepancies in the results emerged, in the Aosta Valley, TESSA reported 423 Gg for OC stock in mixed broadleaves, compared to 263 Gg from field data and 210 Gg from the National Inventory. Fieldwork data collection, while the most accurate, was the most time and resource intensive. The national inventory yielded values similar to fieldwork data; for example, in the Adamello spruce forest, the National Inventory reported 1838 Gg, while field data measured 1964 Gg. However, TESSA depicted qualitatively the same organic carbon stock distribution across the habitats compared to the other approaches. Based on the results, we propose different applications for these approaches, considering the advantages and disadvantages of each. Specifically, we suggest using the TESSA toolkit for preliminary and a qualitative screening of a study area to identify potential areas of interest for the carbon stock, while more precise but demanding approaches should be employed for local studies.