Probiotics can release many bioactive peptides that confer a myriad of benefits to the host health. However, exploring new bioactive peptides secreted by probiotics is hampered by lots of matrix-related interference peptides from the medium, and the low abundance. To this end, a new approach integrating mixed-mode cationic exchange based solid-phase extraction (MCX-SPE) coupled with liquid chromatography-mass spectrometry (LC–MS) and feature-based molecular networking (FBMN) was developed. FBMN's intuitive visualization results enabled twenty-five novel peptides to be quickly discovered and characterized from the cultures of three strains of Bifidobacterium, B. animalis, B. longum, and B. pseudolongum. Interestingly, four were uniquely secreted by B. animalis treated with gypenosides, and one showed ACE inhibitory effect with an IC value of 193.22 μM. Consequently, this approach could serve as a powerful tool for quickly discovering bioactive peptides from the complex metabolites of probiotics, which contributes to the development of functional foods and nutraceuticals.