•This work is the first study about protein changes in smoked dry-cured ham.•Proteolysis and protein oxidation during the smoked dry-cured ham processing was monitored.•Proteolytic changes were more advanced in Biceps femoris than in Semimembranosus.•Protein carbonylation followed the same trend in both muscles.•In-depth research of smoking on protein changes during ham processing was conducted. During the five stages of smoked dry-cured ham processing, proteolysis and protein oxidation were simultaneously detected in the Biceps femoris (BF) and Semimembranosus (SM) muscles. Proteolysis was more advanced in BF than in SM throughout the process of production. The total FAA increased significantly (p < 0.05) throughout the processing, resulting in higher total FAA content in BF than in SM muscle. SDS-PAGE revealed progressive degradation of sarcoplasmic proteins of investigated muscles, with the pronounced changes for the 69.9–41.7 kDa region. SDS-PAGE of BF showed more intense degradation of myofibrillar proteins due to greater proteolysis in BF. Electrophoresis of myofibrillar proteins evidenced the marked degradation of 130 kDa, 96.7 kDa and 27–20.7 kDa bands in both muscles. A similar trend was observed for protein oxidation in BF and SM, with the final values of 26.36 and 23.7 nmol carbonyls/mg proteins, respectively. The Pearson correlation revealed a strong relationship between protein oxidation and proteolysis.