The Gulf of Mexico hydrocarbon seeps are often populated by dense mussel beds and tubeworm aggregations, as well as exposed authigenic carbonate outcrops. Previous studies suggest the activity of mussels and tubeworms could influence the sediment geochemistry of their habitats, resulting in variations in the stable carbon isotopes of the associated carbonates. However, this conclusion was based on the analyses of samples from a single site. To better understand whether there are consistent differences in the geochemical environments of mussels and tubeworms, mineralogical and stable isotopic compositions of authigenic carbonates from mussel and tubeworm environments from four seep sites were analyzed. The studied sites span a depth range of 1200 m to 2800 m on the northern Gulf of Mexico continental slope. We found that carbonate samples from tubeworm environments were more prone to contain aragonite whereas carbonates from mussel environments were more likely to have calcite. This finding supports the hypothesis that vestimentiferans release sulfate across their roots into the pore waters of the surrounding sediments, a process that could generate a locally sulfate-enriched environment that favors the precipitation of aragonite instead of calcite. Moreover, the δ13C values of tubeworm carbonates are generally lighter than that of mussel carbonates from the same site, which is consistent with the fact that tubeworms are fueling extra subsurface methane oxidation through the release of sulfate into the sediment. Such a process, consequently, enriches the subsurface dissolved inorganic carbon pool with light carbon derived from the seeping hydrocarbons. Taken together, our data suggest that tubeworms could produce a carbon isotope shift that is sufficient to influence the sediment geochemistry of their immediate area, and that this impact is reflected in the associated authigenic carbonates.