Peptidomics refers to the comprehensive profiling of endogenous peptides obtained from biological sources. The formation of endogenous peptides is dependent on not only endogenous factors but also exogenous factors such as microbial proteases or process conditions, including fermentation. This study analyzed the probiotic strains of Lactobacillus rhamnosus LOCK900 (LOCK), Bifidobacterium animalis ssp. lactis BB-12 (BB12), and potential probiotic Lactobacillus acidophilus Bauer Ł0938 (BAUER) to assess their ability of fermentation and peptide production in dry-cured pork loin. The peptides obtained after in vitro digestion were characterized by liquid chromatography–tandem mass spectrometry. Based on the sequences identified, the degree of similarity or differences between the peptides was determined and presented graphically on the factor plane. The charts showed that the meat products aged for 180 and 270 days were the most diverse when BB12 or BAUER were used as starter cultures. Myosin and keratin were identified as the most likely precursors of bioactive peptides in products obtained using this strain of lactic acid bacteria (LAB). The knowledge acquired from this study may contribute to the design of functional meat products as the results revealed not only the peptidogenic potential of the LAB strains indicated on their beneficial effect on the bioactivity of peptides.