Several compounds with enhanced functional properties of interest in the nutraceutical and medical sectors can be recovered by using the biomass currently wasted in fishing extractive and processing activities, promoting the sustainability of this sector and leading to its development under a bio-economical framework. In particular, it has been observed that crustaceans are an important fraction of the total biomass discarded by fisheries, mainly in those metiers involving coastal waters. Crustacean biomass can be destined to the production of chitin/chitosan (in combination with food use of muscle or protein hydrolysates production) since their exoskeletons are one of the most important sources of this polysaccharide available for commercial use. In this work, the sustainability of both the chemical and enzymatic process to obtain chitin at pilot scale was analysed. The three sustainability dimensions were evaluated and integrated by hierarchical methods to provide a consistent comparison baseline between processes. The results indicated that the enzymatic process could be an adequate alternative that should be considered for chitin extraction, especially if water recovery is employed.