Mesopelagic species are unexplored novel low‐trophic sources of essential micronutrients and may contribute to combat malnutrition. In this study, common mesopelagic species from the North Sea including Northern krill (Meganyctiphanes norvegica), glacier lanternfish (Benthosema glaciale), and Muller's pearlside (Maurolicus muelleri) were supplemented in mice feed using a Western diet recipe. The metabolic outcomes were subsequently compared to those of ordinary seafood. Consumption of mesopelagic species induced a large variation in weight gain, in the following order: lanternfish (7.1 g) > krill (14.4 g) > control (19.7 g) > pearlside (22.6 g). The lanternfish‐supplemented diet containing wax esters reduced weight gain and obesity and improved insulin sensitivity. The wax esters from the lanternfish‐supplemented diet were efficiently absorbed, with more than 92% of the fatty alcohols being assimilated. The inclusion of lanternfish and pearlside led to improvements in the fatty acid (FA) composition in the mouse liver, evidenced by increased levels of essential long‐chain polyunsaturated FAs and an increased n‐3/n‐6 ratio (0.7 to 1.45 vs. 0.46 in control group). Notably, no adverse effects were found in mice fed pearlside and lanternfish, although an elevated level of fluoride in femur bone was observed in mice fed a diet supplemented with krill followed by reduced sperm concentration and sperm motility. Collectively, our findings underscore the diverse array of metabolic and physiological effects induced by the consumption of mesopelagic species. Furthermore, these species can be considered as good sources of n‐3 FAs and essential vitamins, suggesting their potential value to human nutrition.