Due to their chemical composition, richness in calcium carbonate, chitin, proteins, and pigments, and nanoporous structure, crustacean shell waste shows great potential for a wide variety of applications. Large quantities of waste shells are produced annually, meaning that they can be considered a renewable source of ecofriendly biogenic materials, which can be turned into value-added byproducts. In this paper, an IR-based technique is developed to differentiate various biogenic powders originated from crude or food-processed crustacean shells. The validity of the method is supported by cross-checking with XRD, NMR, and SEM−EDX analyses. Our goal was to determine changes in properties of waste crab shells after the two most common treatments, deproteinization and milling. We discovered that deproteinization with NaOH could be tracked from the IR absorbance intensity ratio of the υ(CH 2,3 ) and υ asym (CO 3 2− ) bands while milling time less influenced this ratio but induced changes in powder particle size distribution and morphology. The relative organic/inorganic ratio was different for different colored shells. Unexpectedly, waste shells stored for an average of 6 months or more were found to contain hydrated calcium carbonate (monohydrocalcite), which was absent in equivalent fresh shell composition. Deproteinization caused changes in mechanical properties of shells, making them more brittle, which resulted in a larger fraction of fine particles after powdering.