The effect of ultra high-pressure homogenisation (UHPH) of goat milk (200 MPa, 30 °C) on the proteolytic profiles of cheese was studied and compared to cheeses made with homogenised-pasteurised (18 + 2 MPa, 72 °C for 15 s) and pasteurised (72 °C, 15 s) milk. Cheeses produced by UHPH-treated milk presented higher hydrolysis of αs2-, β- and para-κ-casein than those made with pasteurised milk; however, cheeses made by homogenised-pasteurised milk exhibited the highest hydrolysis of αs1-and para-κ-caseins. The increase in proteolysis by the homogenisation process could be attributed to the increase in the exposure of substrates to proteolytic enzymes. The UHPH-treatment of milk significantly increased the levels of whey soluble nitrogen and hydrophobic and hydrophilic peptides, however, levels of free amino acids were reduced during the first days of ripening as a consequence of the decrease in the aminopeptidase activity. No significant differences were detected in free amino acid profiles of the different cheeses by the principal component analysis.