Proper diet is critical for laboratory-reared animals, as it may affect not only their welfare, but also experimental results. Amphipods (Crustacea: Amphipoda) play important roles in ecosystems and are often used in environmental research. Endemic amphipods from the ancient Lake Baikal are promising for laboratory bioassays; however, there are currently no laboratory cultures. In this work, we determine how different diets affect the color and metabolism of a laboratory-reared Baikal amphipod, Eulimnogammarus cyaneus. We found that in freshly collected blue-colored animals, body color correlated with total carotenoid content. Total carotenoid levels did not differ after long-term (two months) feeding with a close to natural carotenoid-enriched, or even a carotenoid-depleted diet. Nevertheless, antennae color was closer to red in the natural-like diet group. It is likely that the carotenoids from the commercial diet are not properly metabolized in E. cyaneus. The animals fed commercial diets had a higher glycogen content, which may signify a higher metabolic rate. Overall, we show that a carotenoid-enriched diet optimized for decapods is not optimal for amphipods, likely due to different carotenoid compositions, and the diet for long-term rearing of E. cyaneus and other Baikal amphipods requires supplementation.