<jats:title>Abstract</jats:title><jats:p>Species with effective thermal adaptation mechanisms allowing them to thrive within a wide temperature range can benefit from climatic changes as they can displace highly specialized species. Here, we studied the adaptive capabilities of the Baikal endemic amphipods <jats:italic>Eulimnogammarus verrucosus</jats:italic> (Gerstfeld, 1858) and <jats:italic>Eulimnogammarus cyaneus</jats:italic> (Dybowsky, 1874) compared to the potential Holarctic Baikal invader <jats:italic>Gammarus lacustris</jats:italic> Sars, 1863 at the cellular level including the energy metabolism and the antioxidant system. All species were long-term exposed to a range of temperatures (1.5 °C to mimic winter conditions and the three species-specific preferred temperatures (i.e., 6 °C for <jats:italic>E. verrucosus</jats:italic>, 12 °C for <jats:italic>E. cyaneus</jats:italic> and 15 °C for <jats:italic>G. lacustris</jats:italic>). At 1.5 °C, we found species-specific metabolic alterations (i.e., significantly reduced ATP content and lactate dehydrogenase activity) indicating limitations on the activity level in the Holarctic <jats:italic>G. lacustris</jats:italic>. Although the two Baikal endemic amphipod species largely differ in thermal tolerance, no such limitations were found at 1.5 °C. However, the cold-stenothermal Baikal endemic <jats:italic>E. verrucosus</jats:italic> showed changes indicating a higher involvement of anaerobic metabolism at 12 °C and 15 °C, while the metabolic responses of the more eurythermal Baikal endemic <jats:italic>E. cyaneus</jats:italic> may support aerobic metabolism and an active lifestyle at all exposure temperatures. Rising temperatures in summer may provide a competitive advantage for <jats:italic>G. lacustris</jats:italic> compared to the Baikal species but the inactive lifestyle in the cold is likely preventing <jats:italic>G. lacustris</jats:italic> from establishing a stable population in Lake Baikal.</jats:p>