Oil shale as well as shale oil and shale gas are significant energy resources with huge reserves present in different parts of the world. Various geochemical proxies have been applied to assess the petroleum potential of oil shales with samples pre-treated in various ways, e.g. as whole rock or demineralized sample or as solvent extracted rock/kerogen. In this respect, it is important to understand and quantify, how achieved geochemical parameters are influenced by pre-treatment. In this study, a systematic comparison is presented based on a study on i) whole rock, ii) extracted whole rock, iii) kerogen concentrate, and iv) extracted kerogen concentrate obtained after solvent extraction of demineralized shales. In total, seven immature, organic matter-rich samples from the Miocene lacustrine sediments of the Nördlinger Ries impact crater, Germany, were pretreated in this way leading to overall 28 samples. A set of elemental analysis (C, H, N), Rock-Eval pyrolysis, and Curie Point-pyrolysis–gas chromatography–mass spectrometry measurements were performed on these pretreated samples. Mineral matter removal leads to significant increase of total organic carbon, but also thermally evaporable and pyrolytically cracked organic matter (Rock-Eval S1 and S2 peaks). To some extent, labile organic matter represented in the original S2 peak can be destructed by mineral removal with hydrochloric and hydrofluoric acid, as shown by elevated values of PI [S1/(S1 + S2)] after demineralization. The organic matter type tends to be more petroleum-prone with raised hydrogen index (HI) and aliphaticity values after demineralization, while Rock-Eval Tmax values commonly applied as parameters for thermal maturity tend to decrease, though not for all samples.Reduced TOC, S1, S2 and PI values of extracted samples suggest that both thermally evaporable and additionally some non-evaporable but soluble organic matter hidden in the original S2 peak can be lost after solvent extraction. Increased values of HI, H/C and N/C of extracted samples indicate more oil-prone organic matter types than unextracted samples. Typical maturity-related parameters such as aliphaticity and Rock-Eval Tmax decrease. Smectite and zeolites, which are abundant in the samples, are suggested to protect organic matter to some extent against solvent extraction, influencing a variety of geochemical proxies and the occurrence of metal cation-containing minerals. Zeolite invigorates the protection effect.