The abundance of fish and zooplankton (1 × 109 tons to 7 × 1010 tons) in the mesopelagic zone of the ocean is a source of novel raw materials that provides opportunities for sustainable new product development. The peculiar conditions of light and pressure in this ecological zone and the position of the specific organisms in the marine food chain results in diversity in their bio-composition. Mesopelagic fish are an underutilized resource, rich in proteins and omega-3 oils, and present opportunities to develop novel feed, food and functional food ingredients and products. However, there is also a need to ensure that this resource is not overfished and is processed to optimize the catch in line with sustainability goals. There is therefore a need to establish sustainable bioprocessing technologies to yield value added products from mesopelagic fish species. In the present study, various protein extracts from the mesopelagic fish Maurolicus muelleri (M) and Meganyctiphanes norvegica (Northern Krill) (K) and combinations of proteins from these species (C) were generated using hydrolysis methods. Protein Hydrolysates were generated using four different enzymes including Alcalase, endocut-01, endogenous M/K enzymes and FoodPro PNL. Hydrolysates were characterized and assessed for their ability to inhibit enzymes important in diseases associated with metabolic syndrome. The ability of generated Hydrolysates to inhibit enzymes including Angiotensin-1-converting enzyme (ACE-1; EC. 3.4.15.1) associated with blood pressure regulation, Acetylcholinesterase (AChE; EC 3.1.1.7) associated with maintenance of the nervous system, and Dipeptidyl peptidase IV (DPP-IV; EC 3.4.14.5) linked with development of type-2-diabetes, was determined. In a separate process, the same mesopelagic fish species were transformed into fishmeal, Hydrolysates, fish-silage, and aqueous extracts (AQ) and screened for bioactivities using the same bioassays. The Hydrolysates contained greater than 60% protein (dry weight basis) when analyzed using the DUMAS method. A hydrolysate from M. muelleri generated using FoodPro PNL (M1) inhibited the ACE-1 enzyme by 89.56% when assayed at a concentration of 1 mg/ml compared to the positive control Captopril©. Aqueous extract two (AQ2) inhibited ACE-1 by 95.28% when assayed at 1 mg/ml compared to the control. Sample M1 inhibited DPP-IV by 100% and aqueous extract one (AQ1) inhibited the same enzyme by 90.08% when assayed at a concentration of 1 mg/ml compared to Sitagliptin used as the positive control. All samples assayed did not significantly inhibit the enzyme AChE–fraction C3 (combined hydrolzate 3: Krill and M. muelleri) inhibited AChE by 27.48% only. Based on these results samples M1, C3, and AQ1 were selected for further characterization and the IC50 values for each were determined in relation to ACE-1 and DPP-IV inhibition as well as their amino acid composition. Glutamate and aspartate were the most abundant amino acids in the selected samples. IC50 values of <0.2 mg/ml and distinct terminal amino acids were identified in each of the three fractions. The study shows that targeting processing of mesopelagic fish have potential to generate Hydrolysates for use in the prevention of type-2-diabetes and hypertension.