This research investigated the antioxidant activities and quality characteristics of functional yogurt supplemented with naturally derived protein, specifically lysozyme (LZ), as well as its thermally modified variants PLZ treated at 63°C for 30 minutes (hold type pasteurization method) and BLZ treated at 100°C for 10 minutes (using boiling temperature). Among these variants, the best antioxidant capacity was reported for PLZ, followed by BLZ and LZ. Subsequently, different yogurt samples (YCtrl, YLZ, YPLZ, and YBLZ) were prepared. Through weekly assessments, YPLZ consistently retained the highest antioxidant capacity. Moreover, YPLZ received the highest sensory evaluation scores with the best microbiological quality until the end of the examination period up to 35 days at 4 ±1°C. It was noted that PLZ displayed increased surface hydrophobicity due to gradual thermal denaturation, leading to structural changes and weak cross-dimerization with native milk alpha-lactalbumin in YPLZ. Gel electrophoresis results suggested that proteolysis by lactic acid bacteria (LAB) could facilitate the formation of low-molecular-weight peptides with enhanced antioxidant stability via weak-force dimerization. In conclusion, yogurt fortified with lysozyme, processed using hold-type pasteurization, presents a promising avenue for developing functional yogurt with antioxidant properties.