Fossil coral skeletons that retain their original aragonitic mineralogy are generally considered diagenetically unaltered and reliable paleoenvironmental archives. We investigated whether oxygen isotope exchange can occur between these skeletons and ambient sediment pore water without aragonite-to-calcite transformation, focusing on the role of skeletal microstructure in this process. Simulated diagenesis experiments using modern coral skeletons immersed in 18O-enriched artificial seawater revealed that microstructural complexity – specifically, the phylogenetically controlled arrangement of rapid accretion and thickening deposits – strongly influences isotopic exchange. Organic-rich regions within the skeleton facilitate water penetration, leading to heterogeneous isotopic alteration correlated with skeletal architecture. This provides a mechanism to modify primary isotopic compositions without obvious signs of diagenetic alteration, challenging the assumption that a preserved carbonate polymorph ensures isotopic fidelity in paleoenvironmental reconstructions and complicating the interpretation of the oxygen isotope paleo-temperature proxy in fossil aragonitic biocarbonates. However, we also observed that coral skeletons with less ultrastructural complexity exhibited lower susceptibility to isotope exchange, suggesting a criterium to identify the fossil specimens most suitable for paleoenvironmental analysis.