This study focuses on shell material from Australian pearl oyster (Pinctada maxima) and Pen shell (Pinna bicolor) and the biogenic calcite that composes their outer shell. Previous work on biogenic calcite has established its mechanically superior properties to geological calcite, but does not sufficiently model stress dissipation and toughening on the intercrystalline scale. Through piezo-Raman and microindentation techniques, this study visualizes and quantifies the plastic deformation and toughening mechanisms present in biogenic calcite forms. We establish a linear applied stress-vibrational mode shift relationship for geological, P. maxima, and P. bicolor calcite. We then apply these relationships to the Raman maps of depressions made with a microindenter to create correlative maps of residual stress for each tested material. These maps demonstrate that biogenic calcite structures are able to store comparatively high energy and resist cracking with several toughening mechanisms.