Despite the economic and ecological importance of corals’ skeletal structure, as well as their predicted vulnerability to future climate change, few studies have examined the skeletal mechanical properties at the nanoscale. As climate change is predicted to alter coral growth and physiology, as well as increase mechanical stress events (e.g., bioerosion, storm frequency), it is crucial to understand how skeletal mechanical properties change with environmental conditions. Moreover, while material properties are intimately linked to the chemical composition of the skeleton, no previous study has examined mechanical properties alongside carbonate geochemical composition. Using Porites coral cores from a wide range of reef environments (Thailand, Singapore, Taiwan), we correlated coral’s micro-mechanical properties with chemical composition. In contrast to previous mechanical measurements of reef-building corals, we document unprecedented variability in the hardness, stiffness, and micro-cracking stress of Porites corals across reef environments, which may significantly decrease the structural integrity of reef substrate. Corals from environments with low salinity and high sedimentation had higher organic content and fractured at lower loads, suggesting that skeletal organic content caused enhanced embrittlement. Within individual coral cores, we observed seasonal variability in skeletal stiffness, and a relationship between high sea surface temperature, increased stiffness, and high-density. Regionally, lower Sr/Ca and higher Mg/Ca coincided with decreased stiffness and hardness, which is likely driven by increased amorphous calcium carbonate and skeletal organic content. If the coral is significantly embrittled, as measured here in samples from Singapore, faster erosion is expected. A decrease in skeletal stiffness will decrease the quality of reef substrate, enhance the rate of bioerosion by predators and borers, and increase colony dislodgement, resulting in widespread loss of structural complexity.