This work is focused on applications of Remote Sensing (RS) and Geographic Information Systems (GIS) for forest area analyses and research on the inter-relationship between the state of forest stands, soils, and soil microbial communities. A common database for working in the GIS environment was created for the territory of Vitosha Natural Park (Bulgaria). Differentiation of relatively homogeneous territorial units was achieved via the GIS tools using several base criteria such as the slope, altitude, exposure, soil type, basic rock, and tree composition. Study sites were selected for each territorial unit for field mensuration of the forest stands in sample plots, as well as for taking soil profiles and samples for microbiological analysis. The GIS database for territorial units was supplemented with specialized information on the forest stands from the Vitosha Natural Park management plan. The research of the selected territory with remote sensing was performed by means of automatic classification of satellite data from Sentinel-2. Multiple specially selected vegetation and soil indices were applied for this purpose. The analysis of the field measurements and results from remote sensing for the forest stands indicators show a relation between the soil fertility, soil type, and total microbial count. The studied soil types were classified according to the World Reference Base classification system. The complex analysis proves the inter-relation between the soil type, microbial abundance, and tree species, which are also strongly influenced by the altitude, exposure, and terrain slope.