Purpose. A total sulfur amino acid (TSAA) deficient diet can affect the amino acid composition of skeletal muscles. However, it is unknown how the different muscle proteins are affected by the TSAA deficiency. Methods. The proteomic profiles of the fast-twitch glycolytic longissimus (LM) and the slow-twitch oxidative rhomboideus (RM) muscles were compared in 42-day-old piglets fed either a 28% deficient (TSAA-) or a sufficient (TSAA+) diet in TSAA for 10 days. Differentially regulated proteins were identified and submitted to Gene Ontology Pathways Analysis to identify biological processes affected by TSAA deficiency. Results. A total of 36 proteins in LM and 24 proteins in RM differed in abundance between the two dietary treatments. In both muscles, an increased oxidative energy metabolism was observed in TSAA- piglets. However, a greater mitochondrial oxidation of pyruvate generated from glycolysis was observed in LM of TSAA- piglets, whereas fatty acid beta-oxidation and glycogen sparing were favored in RM. This suggests a muscle-specific reorientation of energy metabolism in response to a TSAA- deficiency. In both muscles, the protein abundance and enzyme activity of superoxide dismutase were increased in TSAA- piglets. Other enzymes involved in antioxidant defense, heat shock proteins coping with cellular stress, and annexins involved in the regulation of apoptosis were generally found to be more expressed in the LM of TSAA- piglets, with no or minor changes in RM. Conclusions. Skeletal muscle proteome in young growing piglets was modulated in a muscle-dependent manner by a deficient TSAA supply, with accentuated changes in fast-twitch glycolytic muscle.