In living organisms, calcium carbonate biomineralization combines complex bio-controlled physical and chemical processes to produce crystalline hierarchical hard tissues (usually calcite or aragonite) typically from an amorphous precursor phase. Understanding the nature of the successive transient amorphous phases potentially involved in the amorphous-to-crystalline transition requires characterization tools, which are able to provide a spatial and spectroscopic analysis of the biomineral structure. In this work, we present a highly sensitive coherent Raman microscopy approach, which allows one to image molecular bond concentrations in post mortem shells and living animals, by exploiting the vibrational signature of the different carbonates compounds. To this end, we target the calcium carbonate vibration mode and produce spatially and spectroscopically resolved images of the shell border of a mollusk shell, the Pinctada margaritifera pearl oyster. A novel approach is further presented to efficiently compare the amount of amorphous carbonate with respect to its crystalline counterpart. Finally, the whole microscopy method is used to image in vivo the shell border and demonstrate the feasibility and the reproducibility of the technique. These findings open chemical imaging perspectives for the study of biogenic and bio-inspired crystals.