Enzymatic modification can effectively improve the gel properties of protein-based food matrices. However, how bacterial proteases influence milk gels has been rarely reported. In the current study, the proteases isolated from two strains of Lactiplantibacillus plantarum, namely YM13–8.1 and YN22–3.1, demonstrated significant improvement in the textural properties of acid-induced gels characterized by increased hardness and a more compact, dense and fine-pored structure. The inclusion of milk-coagulating proteases resulted in a significant augmentation of hydrophobic interactions and disulfide bonds within the protein gels. Furthermore, both proteases exhibited rennet-like characteristics through κ-casein hydrolysis, with key hydrolysis sites identified as Tyr25-Ile26, Ala65-Ala66 and Lys112-Asn113. By utilizing MALDI-TOF-MS, whole genome sequencing and RT-qPCR analysis, we successfully identified the gene responsible for encoding the proteases as prtA, which has not been previously characterized. In conclusion, our findings demonstrate that the newly characterized protease prtA exerts a positive influence on milk gelling.