Allopatric isolation under contrasting environments can drive rapid phenotypic divergence, even over contemporary timescales. Rapid changes in morphology or physiology can allow organisms to adapt to biotic and abiotic characteristics of their habitats. However, multiple types of traits, such as physiological and morphological traits, are rarely jointly considered, although this could reveal adaptation to several selective pressures. We investigated morphological, growth, and metabolic divergence in two allopatric populations of Arctic charr (Salvelinus alpinus) sharing a common evolutionary origin but inhabiting contrasting environments. We combined field observations, common garden and quantitative genetic approaches to disentangle contributions of genetic divergence and plasticity to phenotypic variability. Wild adults differed in body shape and growth trajectories, potentially reflecting plasticity related to resource availability and temperature variations. Under common garden conditions, juveniles displayed inter-population differences in routine metabolic rate, its allometric scaling with body mass, and trophic-related morphology. These patterns suggest divergent selection on physiological and trophic traits. Despite low neutral genetic differentiation, phenotypic divergence unfolded in fewer than 100 years, providing empirical evidence that plasticity and selection can promote rapid multi-trait changes. These findings highlight the importance of integrative, multi-trait approaches to reveal the adaptive potential of small, isolated populations facing rapid environmental change.