An in silico study that featured the effect of starter cultures on the bioactivity and other health benefits of peptides in semi-hard cheese is presented in this contribution. Model Caciotta-type cheese samples were obtained in laboratory conditions in two variations. Sample A included starter cultures of Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris. Sample B included starter cultures of Lactococcus lactis subsp. lactis, Lactococcus lactis subsp. cremoris, and a culture of lactobacilli Lacticaseibacillus casei. The in silico method showed that the peptides inhibited angiotensin-converting enzymes (ACE) and ipeptidyl peptidase IV (DPP-4), as well as possessed antioxidant properties. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris had a greater effect on the formation of bioactive peptides.