Abstract <p>A layer (260–270 cm) of soft carbonate nodules containing numerous valves of ancient diatoms was discovered in bottom sediments of the Bolshaya Zelenovskaya oil-methane seep (Central Baikal). Various methods confirmed the presence of a siderite phase in the carbonate; their enrichment in the heavy isotope δ¹³C (+14‰ VPDB) and the light isotope δ¹⁸O (−8.43‰ VPDB) also has been detected. Carbonate precipitation could have been facilitated by the high organic matter content of ancient diatoms, dissolved inorganic carbon, or CO₂, supplied by the flow of mineralized fluids and formed during methanogenesis. High-throughput sequencing of the variable region of the 16S rRNA gene revealed the dominance of archaea of the family <i>Methanoregulaceae</i> (11–35%) and of the class <i>Bathyarchaeia</i> (16–54%) with a significant contribution of representatives of <i>Nitrososphaeria</i> (18%) and <i>Woesearchaeales</i> (10%) in the surface sample, as well as of <i>Hadarchaeota</i> (12%) in the deep carbonate-containing sediment. Bacterial dominants were represented by the phyla <i>Chloroflexota</i> (14–30%) and <i>Acidobacteriota</i> (5.8–11%), as well as representatives of <i>Pseudomonadota</i> (32%) in the surface sample and of <i>Artibacterota</i> (28.5%) in the carbonate-containing sediment. Based on the isotopic composition of δ¹⁸O and δ¹³C, chemical composition of pore waters, and microbial diversity, the manuscript discusses the possible scenario of carbonate precipitation process.</p>