Accurate mapping of forest habitats, especially in NATURA sites, is essential information for forest monitoring and sustainable management but also for habitat characterisation and ecosystem functioning. Remote sensing data and spatial modelling allow accurate mapping of the presence and distribution of tree species and habitats and are valuable tools for the long-term assessment of habitat status required by the European Commission. In order to serve the above, the present study aims to propose a methodology to accurately map the spatial distribution of forest habitats in three NATURA2000 sites of Cyprus by employing Sentinel-1 and Sentinel-2 data as well as topographic features using the Google Earth Engine (GEE). A pivotal aspect of the methodology identified was that the best band combination of the Random Forest (RF) classifier achieves the highest performance for mapping the dominant habitats in the three case studies. Specifically, in the Akamas region, eight habitat types have been mapped, in Paphos nine and six in Troodos. These habitat types are included in three of the nine habitat groups based on the EU’s Habitat Directive: the sclerophyllous scrub, rocky habitats and caves and forests. The results show that using the RF algorithm achieves the highest performance, especially using Dataset 6, which is based on S2 bands, spectral indices and topographical features, and Dataset 13, which includes S2, S1, spectral indices and topographical features. These datasets achieve an overall accuracy (OA) of approximately 91–94%. In contrast, Dataset 7, which includes only S1 bands and Dataset 9, which combines S1 bands and spectral indices, achieve the lowest performance with an OA of approximately 25–43%.