We sampled and studied a borehole located in the southern part of Maritsa Iztok lignite field (Bulgaria) which comprises Late Miocene-Pliocene sediments of Maritsa Formation. The current report of Troyanovo-3 Mine sequence is the first to our knowledge. It represents a lignite-mudstone succession with variations in organic matter (OM) maturity. Thirty eight coal and mudstone core samples showed predictable ash and sulfur content. The XRD study showed illite/muscovite, illite/smectite, kaolinite, chlorite and quartz as main constituents that argue for a detrital origin. Additionally, we identified pyrite and gypsum and some peaks of marcasite and elemental sulfur. A set of eight mudstone samples rich in OM was selected for further geochemical analyses. The OM was classified as type III and II/III kerogen based on Rock-Eval pyrolysis data. The low amounts of extractable organic matter (0.01–2.25%) we found are consistent with the samples' low maturity and kerogen type. The yields of two samples were too low for further fractionation. Asphaltene amount (26.1–79.7%) predominates in the extracts. Diterpenoids (neutral fraction) and their polar analogues (slightly polar fraction) are highly abundant. In slightly polar fractions we registered ketotriterpenoids (mainly lupenones) in addition to the linear n-alkan-2-ones.OM elevated maturity of the deepest sample (59.60 m depth) was evidenced mainly by hopane distributions, i.e. Ts/(Tm + Ts), homohopane H31αβ index, hopane ratios (H29αβ/H30αβ) and H27β/H27α. The organic geochemistry results do not fit the ordinary regional maturity trend. OM maturity variation, superimposed over natural low coalification degree, could be ascribed to an interaction with ascending hot reductive fluids. The sulfide mineralization found in the fractures also gives indications about the fluid circulation. Another thermal alteration affecting the middle part samples (24.0–28.3 m) was suggested due to elevated Tmax values and HI and OI relation for a charcoal piece and carbonaceous mudstone. Smoldering processes affecting these samples were presumed.Low-temperature alteration processes were identified by n-alkanes, n-alkan-2-ones, and n-alcohols expulsion and downwards migration (from 18.0 m to 30.0 m) accompanied by a clear terpenoids depletion. The 17,21-seco-hopane-17,21-dione found for the first time for Maritsa Iztok Basin (MIB) samples further suggested processes of water seepage and wash-out. Microbial degradation activities usually accompanying water-washing possibly led to a specific n-alkan-2-one distribution. All the features we report point to either an even-numbered n-alkanoic acid decarboxylation or to a selective microbial degradation of odd-numbered n-alkanes to n-alkan-2-ones. In all, the history of the coal-mudstone sequence is complex, overprinted by variable alteration processes, first ever reported for MIB samples.