There is a wide variety of peptides released from food proteins that are able to exert a relevant benefit for human health, such as angiotensin-converting enzyme inhibition, antioxidant, anti-inflammatory, hypoglucemic, or antithrombotic activity, among others. This manuscript is reviewing the recent advances on enzymatic mechanisms for the hydrolysis of proteins from foods of animal origin, including the types of enzymes and mechanisms of action involved, the strategies followed for the isolation and identification of bioactive peptides through advanced proteomic tools, and the assessment of bioactivity and its beneficial effects. Specific applications in fermented and/or ripened foods where a significant number of bioactive peptides have been reported with relevant in vivo physiological effects on laboratory rats and humans as well as the hydrolysis of animal food proteins for the production of bioactive peptides are also reviewed.