A top-down approach to the mineralized structures and developmental steps that can be separated in the shells of Pinctada margaritifera was carried out. Detailed characterizations show that each of the two major layers usually taken into account (the outer prismatic layer and the inner nacreous layer) is actually the result of a complex process during which the microstructural patterns were progressively established. From its early growing stages in the deeper part of the periostracal grove up to the formation of the most inner nacreous layers, this species provides a demonstrative case study illustrating the leading role of specifically secreted organic structures as determinants of the crystallographic properties of the shell-building units. Gathering data established at various observational scales ranging from morphology to the nanometer level, this study allows for a reexamination of the recent and current biomineralization models.