Recently, bioactive peptides as a health-promoting agent have come to the forefront of health research; however, industrial production is limited, possibly due to the lack of the required technological knowledge. The objective of the investigation was to prepare bioactive peptides with hypoallergenic properties from liquid milk protein concentrate (LMPC), through sequential enzymatic and microbial hydrolysis. LMPC was produced from ultra-heat-treated (UHT) skimmed cow’s milk using a nanofiltration membrane. The effect of the concentration of trypsin (0.008–0.032 g·L−1) on the hydrolysis of LMPC was studied. Subsequently, the hydrolysis of tryptic-hydrolyzed LMPC (LMPC-T) with lactic acid bacteria was performed, and the effect of glucose in microbial hydrolysis was studied. Aquaphotomic analysis of the hydrolysis of LMPC was performed using the spectral range of 1300–1600 nm (near-infrared spectra). Changes in antioxidant capacity, anti-angiotensin-converting enzyme activity, and antibacterial activity against Bacillus cereus, Staphylococcus aureus and Listeria monocytogenes were noted after the sequential tryptic and microbial hydrolysis of LMPC. Allergenicity in LMPC was reduced, due to sequential hydrolysis with 0.016 g·L−1 of trypsin and lacteal acid bacteria. According to the aquaphotomic analysis result, there was a dissociation of hydrogen bonds in compounds during the initial period of fermentation and, subsequently, the formation of compounds with hydrogen bonds. The formation of compounds with a hydrogen bond was more noticeable when microbial hydrolysis was performed with glucose. This may support the belief that the results of the present investigation will be useful to scale up the process in the food and biopharmaceutical industries.