AbstractShallow marine thrombolites from a newly discovered Lower Cretaceous cold seep in the Outer Carpathians (Poland) were analysed in order to untangle the complex sedimentological and biogeochemical processes involved in their formation and their diagenetic modifications. The studied thrombolites are made of two components: (i) microcrystalline mesoclots; and (ii) spar‐filled framework cavities. These components are dominated by calcite and show a complex spatial relationship, resulting in a heterogeneous, clotted fabric. The mesoclots exhibit digitate structures, often concentrically‐laminated, and are chiefly composed of microcrystalline material with δ13C values from −34.8 to −19.4‰ PeeDee Belemnite. Biomarkers analyses show the presence of 2, 6, 10, 15, 19‐pentamethylicosane within the mesoclots. The mesoclots host <5 mm wide microtubes filled with isopachous calcite recording even lower δ13C values (from −39.0 to −20.5‰ PeeDee Belemnite). The morphology of the mesoclots relative to their internal lamination and their geochemistry indicates that their growth was linked to anaerobic oxidation of methane while the microtubes acted as conduits for hydrocarbon‐charged fluids. The framework cavities are internally lined with framboidal pyrite, and are cemented by calcite spar with relatively high δ13C (−15.1 to −7.3‰ PeeDee Belemnite) and low δ18O values (−9.3 to −4.4‰ PeeDee Belemnite). Carbonate precipitation within the framework cavities is interpreted to have been related to bacterial sulphate reduction. U‐shaped trace fossils attributed to the ichnogenus Balanoglossites cross‐cut both mesoclots and framework cavities. The mechanisms involved in the formation and diagenesis of thrombolites at cold seeps are yet to be fully understood, and this work provides new insights on these complex biogeochemical and sedimentological processes.