Waste biogenic materials derived from seafood exploitation represent valuable resources of new compounds within the blue bioeconomy concept. Here, we describe the effectiveness of Raman technology implementation as an in-line tool for the demineralization process control of crustaceans or gastropods. Transparent chitin polymeric foils and calcium acetate by-products were obtained from three waste crustacean shells (C. sapidus, S. mantis, and M. squinado) using a slow, green chemical approach employing acetic acid. Progressive mineral dissolution and increasing of the Raman characteristic signal of chitin is shown in a time-dependent manner using NIR-Raman spectroscopy, while resonance Raman shows intact carotenoids in reacted shells after 2 weeks. Chitin foil products are species-specific, and the demineralization bath of the waste shell mixture can be effectively tracked by Raman tools for solvent control and decision making for the recovery of calcium acetate by-products. Comparatively obtained calcium acetate from Rapana venosa snail shells, the subject of Raman analyses, allowed assessing by-product identity, hydration status, purity, and suitability as recrystallized material for further use as a pharmaceutical compound derived from different crustaceans or gastropod species. Cross validation of the results was done using FT-IR, XRD, and SEM-EDX techniques. A hand-held flexible TacticID Raman system with 1064 nm excitation demonstrated its effectiveness as a rapid, in-line decision making tool during process control and revealed excellent reproducibility of the lab-based instrument signal, suitable for in situ evaluation of the demineralization status and solvent saturation control.