Exercise training increases skeletal muscle expression of metabolic proteins improving the oxidative capacity. Adaptations in skeletal muscle by pharmacologically induced activation of 5'AMP-activated protein kinase (AMPK) are dependent on the AMPKα2 subunit. We hypothesized that exercise training-induced increases in exercise capacity and expression of metabolic proteins as well as acute exercise-induced gene regulation would be compromised in AMPKα1 and -α2 muscle-specific double knockout (mdKO) mice. An acute bout of exercise increased skeletal muscle mRNA content of cytochrome C oxidase subunit I, glucose transporter 4 and VEGF in an AMPK-dependent manner, while cluster of differentiation 36 and fatty acid transport protein 1 mRNA content increased similarly in AMPKα wild type (WT) and mdKO mice. During four weeks of voluntary running wheel exercise training, the AMPKα mdKO mice ran less than WT. Maximal running speed was lower in AMPKα mdKO than WT mice, but increased similarly in both genotypes with exercise training. Exercise training increased quadriceps protein content of ubiquinol-cytochrome-C reductase core protein 1 (UQCRC1), cytochrome C, hexokinase II, plasma membrane fatty acid binding protein and citrate synthase activity more in AMPKα WT than mdKO muscle. However, analysis of a subgroup of mice matched for running distance revealed that only UQCRC1 protein content increased more in WT than mdKO mice with exercise training. Thus, AMPKα1 and -α2 subunits are important for acute exercise-induced mRNA responses of some genes and may be involved in regulating basal metabolic protein expression, but seem to be less important in exercise training-induced adaptations in metabolic proteins.