Raised atmospheric emissions of carbon dioxide (CO2) result in an increased ocean pCO2 level and decreased carbonate saturation state. Ocean acidification potentially represents a major threat to calcifying organisms, specifically mollusks. The present study focuses on the impact of elevated pCO2 on shell microstructural and mechanical properties of the bivalve Cerastoderma edule. The mollusks were collected from the Baltic Sea and kept in flow-through systems at six different pCO2 levels from 900 μatm (control) to 24,400 μatm. Extreme pCO2 levels were used to determine the effects of potential leaks from the carbon capture and sequestration sites where CO2 is stored in sub-seabed geological formations. Two approaches were combined to determine the effects of the acidified conditions: (1) Shell microstructures and dissolution damage were analyzed using scanning electron microscopy (SEM) and (2) shell hardness was tested using nanoindentation. Microstructures of specimens reared at different pCO2 levels do not show significant changes in their size and shape. Likewise, the increase of pCO2 does not affect shell hardness. However, dissolution of ontogenetically younger portions of the shell becomes more severe with the increase of pCO2. Irrespective of pCO2, strong negative correlations exist between microstructure size and shell mechanics. An additional sample from the North Sea revealed the same microstructural-mechanical interdependency as the shells from the Baltic Sea. Our findings suggest that the skeletal structure of C. edule is not intensely influenced by pCO2 variations. Furthermore, our study indicates that naturally occurring shell mechanical property depends on the shell architecture at μm-scale.