The rapidly intensifying process of ocean acidification (OA) due to anthropogenic CO2 is not only depleting carbonate ions necessary for calcification but also causing acidosis and disrupting internal pH homeostasis in several marine organisms. These negative consequences of OA on marine calcifiers, i.e. oyster species, have been very well documented in recent studies; however, the consequences of reduced or impaired calcification on the end-product, shells or skeletons, still remain one of the major research gaps. Shells produced by marine organisms under OA are expected to show signs of dissolution, disorganized microstructure and reduced mechanical properties. To bridge this knowledge gap and to test the above hypothesis, we investigated the effect of OA on juvenile shells of the commercially important oyster species, Magallana angulata, at ecologically and climatically relevant OA levels (using pH 8.1, 7.8, 7.5, 7.2). In lower pH conditions, a drop of shell hardness and stiffness was revealed by nanoindentation tests, while an evident porous internal microstructure was detected by scanning electron microscopy. Crystallographic orientation, on the other hand, showed no significant difference with decreasing pH using electron back-scattered diffraction (EBSD). These results indicate the porous internal microstructure may be the cause of the reduction in shell hardness and stiffness. The overall decrease of shell density observed from micro-computed tomography analysis indicates the porous internal microstructure may run through the shell, thus inevitably limiting the effectiveness of the shell's defensive function. This study shows the potential deterioration of oyster shells induced by OA, especially in their early life stage. This knowledge is critical to estimate the survival and production of edible oysters in the future ocean.