Soil structure has an important role in storing and transporting substances, providing natural habitats for soil microorganisms, and allowing chemical reactions in the soil. A complex investigation on factors affecting soil structure characteristics under herbaceous (H), deciduous (D), mixed (M), and coniferous (SP—Scots Pine and NS—Norway Spruce) vegetation was conducted at three experimental stations—Gabra, Govedartsi, and Igralishte, located correspondingly in the Lozenska, Rila, and Maleshevska Mountains in South-West Bulgaria. The data set obtained includes soil structure indicators and physical, physicochemical, chemical, mineralogical, and microbiological parameters of the A and AC horizons of 11 soil profiles. Under different vegetation conditions, soil structure indicators respond differently depending on climatic conditions and basic soil properties. Regarding the plant available water capacity (PAWC), air capacity (AC), and water-stable aggregates (WSAs), the surface soil layers have an optimal structure in Gabra (H, D), Govedartsi (H, SP, NS), and Igralishte (H). The values for the relative field capacity (RFC < 0.6) showed that the studied soils were water-limited. The WSAs correlated with SOC in Gabra, while in Govedartsi and Igralishte, the WSAs correlated with the β-glucosidase known to hydrolyze organic carbon compounds in soil. The information obtained is important for soil quality monitoring under climatic and anthropogenic changes.