Biomineralised hard parts form the most important physical fossil record of past environmental conditions. However, living organisms are not in thermodynamic equilibrium with their environment and create local chemical compartments within their bodies where physiologic processes such as biomineralisation take place. Generating their mineralized hard parts most marine invertebrates thus produce metastable aragonite rather than the stable polymorph of CaCO3, calcite. After death of the organism, the physiological conditions which were present during biomineralisation are not sustained any further and the system moves toward inorganic equilibrium with the surrounding inorganic geological system. Thus, during diagenesis the original biogenic structure of aragonitic tissue disappears and is replaced by inorganic structural features. In order to understand the diagenetic replacement of biogenic aragonite to non-biogenic calcite, we subjected Arctica islandica mollusc shells to hydrothermal alteration experiments. Experimental conditions were between 100 °C and 175 °C with reaction durations between one and 84 days, and alteration fluids simulating meteoric and burial waters, respectively. Detailed microstructural and geochemical data were collected for samples altered at 100 °C (and at 0.1 MPa pressure) for 28 days and for samples altered at 175 °C (and at 0.9 MPa pressure) for 7 and 84 days, respectively. During hydrothermal alteration at 100 °C for 28 days, most but not all of the biopolymer matrix was destroyed, while shell aragonite and its characteristic microstructure was largely preserved. In all experiments below 175 °C there are no signs of a replacement reaction of shell aragonite to calcite in X-ray diffraction bulk analysis. At 175 °C the replacement reaction started after a dormant time of 4 days, and the original shell microstructure was almost completely overprinted by the aragonite to calcite replacement reaction after 10 days. Newly formed calcite nucleated at locations which were in contact with the fluid, at the shell surface, in the open pore system, and along growth lines. In the experiments with fluids simulating meteoric water, calcite crystals reached sizes up to 200 micrometres, while in the experiments with Mg-containing fluids the calcite crystals reached sizes up to one mm after 7 days of alteration. Aragonite is metastable at all applied conditions. A small bulk thermodynamic driving force exists for the transition to calcite, which is augmented by stresses induced by organic matrix and interface energies related to the nanoparticulate architecture of the biogenic aragonite. We attribute the sluggish replacement reaction to the inhibition of calcite nucleation in the temperature window from ca. 50 °C to ca. 170 °C, or, additionally, to the presence of magnesium. Correspondingly, in Mg2+-bearing solutions the newly formed calcite crystals are larger than in Mg2+-free solutions. Overall, the aragonite-calcite transition occurs via an interface-coupled dissolution-reprecipitation mechanism, which preserves morphologies down to the sub-micrometre scale and induces porosity in the newly formed phase. The absence of aragonite replacement by calcite at temperatures lower than 175 °C contributes to explain why aragonitic or bimineralic shells and skeletons have a good potential of preservation and a complete fossil record.