Migration of methane-rich fluids at submarine cold seeps drives intense microbial activity and precipitation of authigenic carbonates. In this study, we analyzed microbially derived authigenic carbonate samples recently recovered from active gas hydrate mounds on the southwestern slope of the Chukchi Borderlands (CB), western Arctic Ocean. Our main aim was to characterize the distribution patterns of trace elements in carbonate-hosted lipid fractions to assess metalloenzyme requirements of microbes involved in anaerobic oxidation of methane (AOM). We measured stable isotopes, trace elements, lipid biomarkers, and genomic DNA, and results indicate the dominance of AOM-related lipid biomarkers in studied carbonate samples, as well as a predominant occurrence of the anaerobic methanotrophic archaea (ANME)-1. We also report evidence for significant preferential enrichments of various trace elements (Li, Ni, Co, Cu, Zn, and Mo) in the total lipid fractions of CB carbonates, relative to elemental compositions determined for corresponding carbonate fractions, which differ from those previously reported for other seep sites. We hypothesize that trace element enrichments in carbonate-hosted lipid fractions could vary depending on the type of AOM microbial assemblage. Additional work is required to further investigate the mechanisms of lipid-bound trace elements in cold seep carbonates as potential metalloenzymes in AOM.