Priority habitat types (HTs) within the Natura 2000 network are of the highest importance for conservation in Europe. However, they often occur in smaller areas and their conservation status is not well understood. One such HT is that of the Tilio–Acerion forests of slopes, screes and ravines (9180*). The Natura 2000 study site, Boč–Haloze–Donačka gora, in the Sub-Pannonian region of eastern Slovenia is characterized by a matrix of European beech forests and includes rather small, fragmented areas covered by Tilio–Acerion forests. The goal of this research was to examine the heterogeneity and conservation status of the selected HT through field mapping, which was performed in the summer of 2020. As the conservation of HT calls for a more detailed approach, we distinguished between the following four pre-defined habitat subtypes: (i) Acer pseudoplatanus-Ulmus glabra stands growing mostly in concave terrain, (ii) Fraxinus excelsior stands growing on slopes, (iii) Tilia sp. stands with thermophilous broadleaves occurring on ridges and slopes, (iv) Acer pseudoplatanus stands occurring on more acidic soils with an admixture of Castanea sativa. Field mapping information was complemented with the assessment of habitat subtype characteristics using remote sensing data. The results showed that habitat subtypes differed significantly in terms of area, tree species composition, forest stand characteristics, relief features and the various threats they experienced (e.g., fragmentation, tree mortality, ungulate browsing pressure). The differences between subtypes were also evident for LiDAR-derived environmental factors related to topography (i.e., terrain steepness and Topographic Position Index). This study provides a baseline for setting more realistic objectives for the conservation management of priority forest HTs. Due to the specificities of each individual habitat subtype, conservation activities should be targeted to the Natura 2000 habitat subtype level.