We present evidence of exceptional preservation in the nacre and prismatic layers of a 66 Ma bivalve shell using photoemission electron spectromicroscopy (PEEM). PEEM is a novel method to assess in situ the quality of mineralogical and organic preservation. The analysis is non-invasive and non-destructive, providing spatially explicit maps of microstructure, organics and mineral components, and the crystallographic orientation in mollusk shells. Comparison of a Late Cretaceous and a modern shell demonstrates that the 66 Ma shell (1) preserves original aragonite and calcite crystals in nacre and prismatic layers, respectively, (2) maintains nearly identical mineral microstructure and crystal orientations, and (3) preserves interprismatic proteins. Remarkably, interprismatic proteins are preserved with intact peptide bonds, and suggest an abundance of the amino acid glycine. These findings in a 66 Ma shell support the exceptional quality of organic preservation documented here, which may prove to be relatively common among fossil shells that preserve nacre. PEEM analysis is useful for understanding taphonomic processes influencing shell and molecular fossil preservation over geologic time scales, and contributes to our knowledge of molluscan physiology, biomineralization, evolution, and diagenesis.