This study aimed to characterize and compare the muscle proteomes of goat Longissimus thoracis (LT) and Semitendinosus (ST) muscles taken early post-mortem from young crossbred males. Thanks to a quantitative proteomics approach, 129 differentially expressed proteins (DEPs) were identified. The proteins belong to five interconnected biological pathways: muscle contraction and structure (n = 47), catalytic, metabolism & ATP processes (n = 33), binding and transport (n = 23), oxidative stress and cell redox homeostasis (n = 10), response to stress and protein folding (n = 6). An additional group of miscellaneous proteins (n = 10) grouped proteins playing other functions. The chemometrics analyses allowed clear separations of the muscles and evidenced 14 common proteins (ACTB, ACTN3, TMOD4, TPM3, TNNT1, AK1, AKR1B1, ACAA2, GPI, AGL, DNPEP, RTN4, ATP2A1, and CAVIN4) that could be considered as potential biomarkers. Overall, the study provided the first insights on the differences between goat LT and ST muscles and the basis related to the regulation of the skeletal muscle. Moreover, it resulted that a better understanding of the muscle characteristics would help in developing practices/processes to monitor meat quality and reduce the variations in fresh quality of meat, aged meat, and/or processed goat meat products.