The effects of UV-C light irradiation and low-temperature long-time (LTLT) pasteurization on protein structural changes, degree of hydrolysis (DH) by trypsin, peptide profile of tryptic hydrolysates by MALDI-TOF/TOF-MS, and bioavailability of β-lactoglobulin were compared. Compared with native or LTLT pasteurised samples, the hydrolysis rate constant of β-lactoglobulin treated with UV-C increased significantly, implying that the protein backbone cleavage sites became more accessible, whereas thermal treatment produced aggregates that impede trypsin activity. Tryptic hydrolyses of UV-C light treated β-lactoglobulin yielded more peptides and a more diverse peptide mass profile. Six bioactive peptides were revealed in β-LG tryptic hydrolysates of UV-C-treated protein; transepithelial transport in Caco-2 cell monolayers showed intermediate in vivo transport and absorption for three (β-LG f_87–91, β-LG f_91–99, and β-LG f_158–164). The moderate allergen peptide LSFNPTQLEEQCHI β-LG was absent after tryptic hydrolysis of UV-C-treated protein, indicating that UV-C photolysis may be a useful tool for allergenicity reduction.