Impressive, several meters high tubular concretions in shallow marine calcareous sands and sandstones represent part of the well-exposed, subsurface plumbing network of an Early Eocene methane seep system in the Balkanides foreland (Pobiti Kamani area, Varna, NE Bulgaria). An integrated approach, including petrography, inorganic geochemistry and lipid biomarker analyses was used to reconstruct the evolution of pore fluids and cementation conditions during tube formation and particularly, the role of methane-related carbonate diagenesis. Host sediment lithification from marine pore waters was perturbed soon after deposition by oxidation of predominantly microbial methane causing pervasive cementation by a 13C-poor, homogeneous calcite cement (δ13C values as low as − 44.5‰ V-PDB). The importance of microbially mediated anaerobic oxidation of methane (AOM) is confirmed by extremely 13C-depleted archaeal biomarkers (δ13C values as low as − 123‰ V-PDB). A suite of macrocyclic dialkyl glycerol diethers (MDGD-0 to -2) and sn-3-hydroxyarchaeol comprises a characteristic trait of the Eocene tubular concretions and might represent molecular fossils of so far unknown methane-oxidizing archaea (ANME). Subsurface calcite cementation surrounding the ascending methane plume, resulted from the changing pore water chemistry in response to AOM and could have, on a local scale, been encouraged by the concurrent alteration of detrital feldspar. Fluctuating δ13C (up to − 8‰ V-PDB) and δ18O (− 0.5 to − 9‰ V-PDB) signatures within a single tubular sandstone concretion are at least partly the consequence of isotopic resetting during late meteoric water circulation.