In the Karst region near Divača, Slovenia, soils are developed on the limestone of three geological formations: Sežana, Lipica, and Liburnian. In each formation, six soil profiles were dug, limestone insoluble residua was obtained, and in Liburnian Formation interbedded material and material filling fractures and cavities was sampled. All soils have silty clay and silty-clayey loam texture, pH levels in the range 4.5–7.0, high organic matter content and saturation with basic cations over 50%. However, soils on the Sežana Formation are deeper and more evolved, and besides as Rendzic Phaeozem classify also as Eutric Cambisol. Their insoluble residuum is richest in mineral part. The profiles on the Lipica Formation are a Rendzic Phaeozem, and the shallowest soils on the Liburnian Formation are either a Rendzic Phaeozem or a Rendzic Leptosol. Additionally, the soils formed over the Lipica Formation are characterised by a greater portion of the small rock fragments (<200 g), due to its paleo-karstification. The insoluble residuum of all three formations is rich in organic matter and fine grained. The general soil chemistry is in accordance with highly weathered upper crustal material and, compared to insoluble residua indicates the contribution of material from an additional source. The analysis of variance demonstrated differences in redox-sensitive elements (Cr, Mo, Ni, U, V, and Y) between formations, which are inherited by the insoluble residua. The insoluble residua contributed material and left a specific geochemical fingerprint in the observed soils, but regarding texture and general geochemistry, non-carbonate material must have been added. The material that fills karst forms inside the limestone profile is similar to the soils, but not identical. Other interbedded and probably also eolian material contributed to the final mass. Display omitted •Soils are classified as Rendzic Leptosol, Rendzic Phaeozem and Eutric Cambisol.•Soils are homogeneous in pedological properties and mineral composition.•The limestone of all three formations is pure and insoluble residuum organic matter rich.•Limestone formations influence soil depth and leave geochemical fingerprint.•The contribution of different interbedded and eolian material is probable.