Carbonates that exhibit obvious diagenetic alteration are usually excluded as archives in palaeoenvironmental studies. However, the potential impact of microbial alteration during early diagenesis is still poorly explored. To investigate the sensitivity of sulphur concentration, distribution, oxidation state and isotopic composition in marine aragonite to microbial alteration, Arctica islandica bivalves and Porites sp. corals were experimentally exposed to anaerobic microbial activity. The anoxic incubation media included a benthic bacterial strain Shewanella sediminis and a natural anoxic sediment slurry with a natural microbial community of unknown species. Combined fluorescence microscopy and synchrotron-based analysis of the sulphur distribution and oxidation state enabled a comparison of organic matter and sulphur content in the two materials. Results revealed a higher proportion of reduced sulphur species and locally stronger fluorescence within the pristine bivalve shell compared to the pristine coral skeleton. Within the pristine bivalve specimen, reduced sulphur was enriched in layers along the inner shell margin. After incubation in the anoxic sediment slurry, this region revealed rust-brown staining and a patchy S^2- distribution pattern rather than S^2--layers. Another effect on sulphur distribution was rust-brown coloured fibres along one growth line, revealing a locally higher proportion of sulphur. The δ³⁴S value of carbonate-associated sulphate remained largely unaffected by both incubation media, but a lower δ³⁴S value of water-soluble sulphate reflected the degradation of insoluble organic matter by microbes in both experiments. No significant alteration was detected in the coral samples exposed to microbial alteration. The data clearly identified a distinct sensitivity of organically bound sulphur in biogenic aragonite to microbial alteration even when 'traditional' geochemical proxies such as δ¹⁸O_CARB or δ¹³C_CARB in the carbonate did not show any effect. Differences in the intensity of microbial alteration documented are probably due to inherent variations in the concentration and nature of original organic compositions in the samples.