The earliest diagenetic post‐mortem exposure of biogenic carbonates at the sea floor and in the uppermost sediment column results in the colonization of hard‐part surfaces by bacterial communities. Some of the metabolic redox processes related to these communities have the potential to alter carbonate shell properties, and hence affect earliest diagenetic pathways with significant consequences for archive data. During a three‐month in vitro study, shell subsamples of the ocean quahog Arctica islandica (Linnaeus, 1767) were incubated in natural anoxic sediment slurries and bacterial culture medium of the heterotrophic Shewanella sediminisHAW‐EB3. Bulk analyses of the liquid media from the Shewanella sediminis incubation revealed an over ten‐fold increase in total alkalinity, dissolved inorganic carbon and Ω_Aragonite, and the alteration of the Mg/Ca, Mg/Sr and Sr/Ca ratios relative to control incubations without cultures. Ion ratios were most affected in the incubation with anoxic sediment, depicting a 25% decrease in Mg/Ca relative to the control. Shell sample surfaces that were exposed to both incubations displayed visible surface dissolution features, and an 8 wt% loss in calcium content. No such alteration features were detected in control shells. Apparently, alteration of shell carbonate properties was induced by microbially driven decomposition of shell intercrystalline organic constituents and subsequent opening of pathways for pore fluid–crystal exchange. This study illustrates the potential influence of benthic bacterial metabolism on biogenic carbonate archives during the initial stages of diagenetic alteration within a relatively short experimental duration of only three months. These results suggest that foremost the biological effect of bacterial cation adsorption on divalent cation ratios has the potential to complicate proxy interpretation. Results shown here highlight the necessity to consider bacterial metabolic activities in marine sediments for the interpretation of palaeo‐environmental proxies from shell carbonate archives