Yoghurt supplemented with peach is a dairy product consumed around the world with a shelf-life of ca. 30 days. During this period protein–polyphenol complexes can be formed and have a detrimental effect on the in vivo solubility of both phenolic and proteins. Yoghurt enriched with peach preparate were produced and stored up to 28 days at 2 °C. Total antioxidant activity decreased 24%, total carotenoids increased 66%, while total phenolics remained unchanged during the yoghurt shelf-life. Carotenoids presented significant differences between peach enriched yoghurt and peach preparate stored under the same conditions. After 28 days the zeaxantin + lutein, β-cryptoxanthin and β-carotene increased 133, 122, and 84% respectively, for peach preparate, while in peach yoghurt they increased 68, 40, and 15%, indicating interactions of carotenoids with matrix components mainly proteins and fat present in yoghurt. Polyphenols presented higher stability when added to yoghurt with slight variations in their content of ca. 10% for (+)-catechin and 12% for p-coumaric acid, and no variations were recorded in neochlorogenic and chlorogenic acids and in rutin. The α-lactalbumin content decreased 22% after 24 h of peach addition while β-lactoglobulin content did not change. Peach polyphenols were very stable during yoghurt shelf-life while carotenoids were the compounds that presented higher interactions with the matrix.