•Clay-rich soils on limestones from the Dinaric Karst region are classified as Luvisols.•Illuvial processes explain differences in the geochemical and mineral composition of horizons.•Allochthonous contributions from different sources influence the formation of Luvisols.•Pedogenesis prevails over heterogeneity of profile sites and contribution of allochthonous material.•Well-developed soil horizons indicate intense pedogenetic processes. In environments with high precipitation, eluvial–illuvial processes play a key role in pedogenesis. Vertical translocation of clay leads to the formation of an argic horizon. Such soils are of global importance and formed on different rock substrates under different climatic conditions. However, the pedogenesis of clay-rich soils developed on limestone in humid temperate climates has not been sufficiently investigated. Therefore, this study aimed to evaluate the geochemical and mineral compositions and properties of Luvisols (10 profiles) from the Dinaric karst region and identify the geochemical indicators of eluvial–illuvial processes. The geochemical and mineral differences between the A, E, and Bt horizons could be explained by the pedogenic processes of biorecycling, migration, isomorphic substitution in minerals, surface adsorption to clay or Al/Fe oxide minerals, and precipitation from the soil solution. Illuviation is evident in the downward increase in Al2O3, Fe2O3, MgO, K2O, Ba, Co, Cr, Ga, Ni, Sc, Th, U, V, Y, and REE. Despite differences in the geochemical characteristics of the 10 studied profiles, eluvial–illuvial processes outweighed the heterogeneity of the soils from different sites and the probable contribution of allochthonous material to the soil. We established new textural and geochemical indicators that could explain the differences among horizons and profiles in light of the polygenetic origin of soil material and pedological processes.