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It is important to utilize the entire animal in meat and fish production to ensure sustainability. Rest raw materials, such as bones, heads, trimmings, and skin, contain essential nutrients that can be transformed into high-value products. Enzymatic protein hydrolysis (EPH) is a bioprocess that can upcycle these materials to create valuable proteins and fats. This paper focuses on the role of spectroscopy and chemometrics in characterizing the quality of the resulting protein product and understanding how raw material quality and processing affect it. The article presents recent developments in chemical characterisation and process modelling, with a focus on rest raw materials from poultry and salmon production. Even if some of the technology is relatively mature and implemented in many laboratories and industries, there are still open challenges and research questions. The main challenges are related to the transition of technology and insights from laboratory to industrial scale, and the link between peptide composition and critical product quality attributes. • Spectroscopy and chemometrics are crucial tools for understanding bioprocesses. • Raw material properties and process settings both affect the end-product quality. • NIR and Raman spectroscopy may be used for in-line characterisation of raw materials. • FTIR, SEC and NMR provide detailed characterisation of protein hydrolysates. • Transition of technology and insights from lab to industry is a remaining barrier. [ABSTRACT FROM AUTHOR]