Crustaceans are an economically important group of aquatic sources highly consumed; however, large volumes of waste are generated with potential environmental damage. Crustaceans such as barnacles, crabs, krill, lobster, shrimp, and other waste are a rich source of bioactive compounds such as bioactive peptides, carotenoids, phenolic compounds, polyunsaturated acids, and vitamins. Bioactive compounds from crustacean waste have important properties such as antioxidant activity, antimicrobial, anti-inflammatory, antitumor, lipid-lowering, and hypoglycemic properties. However, the extraction of these compounds is thought to be chemical reagents that large volumes of water have been needed; therefore, novel biotechnological processes have proved to enhance the extraction of the bioactive compounds. Several extraction technologies are promising for the large-scale treatment of crustacean wastes, such as enzymatic fermentation extraction, ultrasound-assisted microwave extraction, and supercritical fluids, to minimize waste elimination and add value to these sub-products. This chapter aims to inform the potential of novel biotechnological processes (liquid fermentation and enzymatic processes) to optimize the extraction of the different bioactive compounds from crustacean wastes.