To assess bioaccessible and dialysable apple polyphenols available for potential uptake by intestinal epithelial cells, an in vitro gastrointestinal (GI) digestion method was developed and main polyphenols investigated by UPLC. Polyphenolic profiles in the gastric medium were similar to those natively occurring in apples; however, bioaccessible polyphenols were at lower concentrations than those in the apples. The polyphenolic profile was altered during intestinal digestion, with a considerable decrease of total polyphenols. Flavan-3-ols were completely unstable in the intestinal medium, owing to their pH sensitivity. In addition, 41–77% of bioaccessible chlorogenic acid, the major abundant hydroxycinnamic acid in apples, was degraded during intestinal digestion, with partial isomerisation to cryptochlorogenic acid and neochlorogenic acid. All polyphenols found in the intestinal medium were dialysable, but were present at lower concentrations, suggesting that dialysable polyphenols can potentially be taken up by the enterocytes. These results highlight that GI digestion may substantially affect native apple-derived polyphenolic patterns and concentrations.