In recent years, fermentation has evolved into a prominent method for the production of bioactive peptides particularly for the development of novel nutraceuticals and functional foods. Microbial proteases breakdown protein into peptides during fermentation, but what happens to the other non-protein components of the fermentation medium? Can microorganisms be grown solely on protein substrate? Milk fermentation, for example, results in the breakdown of milk proteins into peptides; but what about other components? Bacteriocins, which are antimicrobial peptides synthesized by ribosomes rather than milk proteins, are also produced by lactic acid bacteria. Can we claim bioactivity of fermented milk due to bioactive peptides in this case? Other metabolites and bacteriocins have bioactivities as well.