The aim of the present work was to compare microstructure in strong and weak scallop Pecten maximus shells of cultured and wild origin using observations from scanning electron microscopy (SEM) and atomic force microscopy (AFM). The scallops representing the strongest and the weakest shells from each origin and age were selected for the microstructure observations. SEM observations showed various abnormalities of the microstructure, whereas AFM observations did not reveal any abnormalities of the nanostructure. The observed abnormalities were separated into two categories: irregularities and modifications. Irregularities were not directly linked to the microstructure and included bubbly sheets, bacteria, sponge, and hexagonal shapes on the inner layer. Modifications were directly linked to the microstructure and included irregular laths, crystal fragments, and severely modified granule layer covering the myostracal layer. Although irregularities were observed in samples of both cultured and wild P. maximus shells, modifications of the microstructure were observed only in those of cultured origin. Abnormalities were observed more frequently in four- and five-year-old scallop shells, whereas no abnormalities were observed in any of the shell samples from one-year-old scallops. These results suggest that abnormalities in scallop shells develop over time and that cultured scallops seem to be more at risk to develop modifications in microstructure compared with wild scallops. To be able to optimize conditions in aquaculture procedures, more investigation is needed on how the culture environment influence the biomineralization process in hard shelled molluscs.