Collagen peptides (CP) have been used as functional foods for enhancing skin and joint health. Further degradation of CP results in peptide sizes small enough to enter the bloodstream following absorption in the small intestine. We examined the effects of food matrices on CP degradation into short chain peptides and absorption efficiency after ingestion. Changes to hydroxyproline (Hyp)-containing peptide levels in CP after yogurt fermentation and in human plasma by co-ingestion of CP and yogurt, with or without fermentation, were evaluated by liquid chromatography-mass spectrometry (LC-MS). The fermentation of CP with yogurt resulted in the significant degradation of CP into several Hyp-containing peptides such as Ala-Hyp, Leu-Hyp, Phe-Hyp, Ala-Hyp-Gly, and Leu-Hyp-Gly. CP ingestion after yogurt fermentation significantly increased the plasma concentrations of Phe-Hyp, cyclo(Ala-Hyp), and cyclo(Pro-Hyp) compared to water-based CP ingestion. The co-ingestion of CP and yogurt without fermentation significantly increased the plasma levels of Ala-Hyp, Phe-Hyp, Ala-Hyp-Gly, Leu-Hyp-Gly, Pro-Hyp-Gly, cyclo(Ala-Hyp), cyclo(Glu-Hyp), and cyclo(Pro-Hyp). Overall, the co-ingestion of CP and yogurt with or without fermentation significantly enhanced the absorption of CP-derived peptides, represented by the high C_max and area under the curve per 1 h (AUC, nmol/h·mL) of Hyp-containing peptides. These results suggest that, in addition to increasing short chain Hyp-containing peptide levels via fermentation, yogurt matrices containing milk-derived peptides and/or lactic acid bacteria-derived peptidases may influence the efficient absorption of CP-derived peptides into human blood.