Present-day activity of cold seeps in the ocean is evident from direct observations of methane emanating from the seafloor, the presence of chemosynthetic organisms, or the quantification of high gas concentrations in sediment pore waters and the water column. Verifying past cold seep activity and biogeochemical characteristics is more challenging but may be reconstructed from proxy records of authigenic seep carbonates. Here, we investigated the lipid-biomarker inventory, carbonate mineralogy, and stable carbon and oxygen isotope compositions of seep-associated carbonates from two active Arctic methane seeps, located to the northwest (Vestnesa Ridge; ∼1,200 m water depth) and south (Storfjordrenna; ∼380 m water depth) offshore Svalbard. The aragonite-dominated mineralogy of all but one carbonate sample indicate precipitation close to the seafloor in an environment characterized by high rates of sulfate-dependent anaerobic oxidation of methane (AOM). In contrast, Mg-calcite rich nodules sampled in sediments of Storfjordrenna appear to have formed at the sulfate-methane-transition zone deeper within the sediment at lower rates of AOM. AOM activity at the time of carbonate precipitation is indicated by the ¹³C-depleted isotope signature of the carbonates [−20 to−30‰ Vienna Pee Dee Belemnite (VPDB)], as well as high concentrations of ¹³C-depleted lipid biomarkers diagnostic for anaerobic methanotrophic archaea (archaeol and sn2-hydroxyarchaeol) and sulfate-reducing bacteria (iso and anteiso-C15:0 fatty acids) in the carbonates. We also found ¹³C-depleted lipid biomarkers (diploptene and a 4α-methyl sterol) that are diagnostic for bacteria mediating aerobic oxidation of methane (MOx). This suggests that the spatial separation between AOM and MOx zones was relatively narrow at the time of carbonate formation, as is typical for high methane-flux regimes.The seep-associated carbonates also displayed relatively high δ¹⁸O values (4.5–5‰ VPDB), indicating the presence of ¹⁸O-enriched fluids during precipitation, possibly derived from destabilized methane gas hydrates. Based on the combined isotopic evidence, we suggest that all the seep carbonates resulted from the anaerobic oxidation of methane during intense methane seepage. The seepage likely was associated to gas hydrates destabilization, which led to the methane ebullition from the seafloor into the water column.