Meat is an appropriate source of proteins and minerals for human nutrition. Technological treatments modify the physical-chemical properties of proteins, making them liable to decrease the nutritional potential of meat. To counteract this damage, antioxidants and chaperone proteins in muscle cells can prevent oxidation, restore the function of denatured proteins, and thus prevent aggregation. This study aimed to explore the impact of indoor vs outdoor-reared meat protein composition on digestion and to associate protein markers to in vitro digestion parameters. Indoor-reared meat tended to show less oxidation and denaturation than outdoor-reared meat and was characterised by an overexpression of contractile and chaperone proteins. Outdoor-reared meat showed amplification of antioxidant and detoxification metabolism defending against oxidised compounds. Impacts on digestion remained minor. Several protein markers of in vitro digestion parameters were found for aged and cooked meat, linked to the detoxification process and to muscle contraction.