Mollusk shells represent important archives for paleoclimatic studies aiming to reconstruct environmental conditions at high temporal resolution. However, the shells, made of calcium carbonate in the form of aragonite and /or calcite, can be altered through time which may undermine the suitability for any reconstruction based on geochemical proxies (i.e., stable isotopes, radiocarbon). At present, the diagenetic processes involved in this chemical and physical deterioration are still poorly understood. The present study aims to shed light on the onset and development of diagenetic alteration in the aragonitic shell of Phorcus turbinatus. To artificially mimic diagenesis, shells of P. turbinatus were exposed to elevated temperatures. The transformation of the mineral phase was monitored by means of Confocal Raman Microscopy whereas the structural changes were investigated using Scanning Electron Microscopy and Atomic Force Microscopy. The results indicate that the two distinct shell layers (prismatic layer and nacre) respond differently to the elevated temperatures, suggesting that the different microstructural organization and organic content may drive the onset and spread of the aragonite-to-calcite transformation. Furthermore, changes in the microstructural arrangement became visible prior to the mineralogical transition. Our results demonstrate that the specific physico-chemical characteristics of structurally different areas within the biogenic carbonates have to be taken into account when studying the phase transformation occurring during diagenesis.