Seeping of methane-rich fluids at submarine cold seeps drives intense microbial activity and precipitation of authigenic carbonates. Some trace elements play an important role in the biogeochemical processes operating at cold seeps, especially as specific enzymatic co-factors related to methanogenesis and the anaerobic oxidation of methane (AOM). However, it is unclear whether microbial trace metal utilization can be traced by the geochemical composition of seep carbonates. In this study, we analyzed a series of authigenic carbonate samples recovered from various seep settings worldwide and report for the first time trace element concentrations for total lipid fractions, combined with biomarker analyses and determination of elemental abundances in associated inorganic mineral phases (carbonate phases, sulfides, organic compounds and detrital fractions). Our results indicate marked enrichments of Co, Ni, Cu, Mo and W in the archaeal and bacterial lipids associated with authigenic carbonates, which can all be ascribed to previously identified enzymatic pathways. In addition to the microbial communities involved in AOM, which most likely control specific lipid-bound enrichments of Co, Ni, Mo and W in seep carbonates, Cu was found to display higher concentrations in the lipid fractions extracted from a few authigenic carbonate samples formed closer to the sediment-water interface, hence possibly related to the presence of aerobic methane-oxidizing bacterial assemblages in the near seafloor environment. While the above mentioned trace metals are relatively enriched in all studied inorganic and organic fractions, the very low W concentrations measured in carbonate phases, combined with their pronounced enrichment in associated lipid fractions and inferred microbial requirement, suggest that tungsten depletion in pore waters could possibly act as a limiting factor on AOM at cold seeps. Finally, two other trace elements (Li and Ti) also displayed particular enrichments in studied lipid fractions, which, despite no reported evidence, could possibly indicate that they are also involved as metalloenzymes in microbial methane oxidation processes at cold seeps.