The purpose of this study is to characterize sedimentologically and isotopically authigenic mineralization and low-rank coals (lignite) from the Velenje basin, Slovenia. Six structural types of calcite mineralization in a fine lignite gelified matrix were recognized, namely: (A) laminae and thin beds, (B) small lenses and lenticular bodies, (C) dispersed mineral matter in minute detritus, (D) calcite-substituted xylite fragments, (E) encrusted xylite fragments, and (F) calcite-coated and calcite-filled pores. Scanning electron microscopy revealed that in parts the calcified lignite is almost pure calcite. The carbon (–4.3 to +16.4‰) and oxygen (–14.5‰ to –6.6‰) isotopic composition indicates a carbonate precipitation temperature of between 5.7 and 45.5°C. The δ13Corg. values and δ15Nbulk of organic compounds were from –29.4‰ to –23.7‰ and from +1.8‰ to +5.9‰, respectively. The lower δ13Corg. values (up to –29.4‰) in the Velenje lignite indicate a high degree of gelification, while the δ15Nbulk values (up to +5.9‰) are indicative of intense mineralization. Furthermore, a carbon isotope fractionation factor (εTOC) of more than 32% suggests that unlike in recent lake sediments from Slovenia, Croatia, and Argentina, where oxic processes dominate, there was intense microbial activity (methane formation in anoxic conditions). In addition, the εTOC values in the Velenje samples are unrelated to mineralization type but are related to the degree of gelification (bacterial activity). The investigation of mineral occurrence is important since cleat-filling minerals reduce coal permeability, which in turn can trigger gas outbursts and inhibit gas extraction.