Fruit and vegetables (F&V) polyphenols have numerous positive health effects, ascribed either to their antioxidant activity within the gastrointestinal tract (GIT) or to bioactivity of their absorbed metabolites. The effect of the F&V matrix on the gastrointestinal bioaccessibility of polyphenols was investigated along with its possible interaction with protein digestion. Minipigs were fed a complete meal with either cubed F&V (apple, plum, artichoke) added, or the corresponding phenolic extract (PE). Gastric and ileal chymes were kinetically collected over the postprandial period. The overall polyphenol bioaccessibility in the stomach was found to be 1.5% and 3.1% after F&V and PE consumption, respectively. The lower release rate from artichoke than from apple showed evidence of a plant effect. Flavanol monomers and glucoside conjugates were not recovered in the ileum in agreement with their absorption in the upper GIT. Interestingly, PE, but not F&V, significantly decreased the speed and efficiency of dietary protein digestion.