Grain polyphenols are known to possess several health properties. However, their digestive stability and intestinal absorption have not been fully elucidated. This study investigated the fate of pigmented grain polyphenols in the digestive system. Purple rice, purple barley, purple wheat, and blue wheat extracts were subjected to simulated gastric and intestinal phase digestion, followed by Caco-2 cellular transport. Phenolic profiling and antioxidant activity were determined using benchtop assays and an ultra-high-performance liquid chromatography-2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid free radical) (UHPLC-ABTS•+) system. The results demonstrated a decrease in the total phenolic content of extracts after digestion, with purple rice extract retaining the highest phenolic content (79%) and ABTS•+antioxidant activity (31%). Antioxidant activity was retained the most during the gastric phase; however, dominant antioxidant compounds were not detected after intestinal digestion. Significant variations in phenolic composition and radical scavenging activity were detected after digestion. Protocatechuic acid, vanillic acid, apigenin, and chrysoeriol were all transported across the intestinal barrier. The findings of this study provide novel insights into the in vitro stability and antioxidant activity of cereal grain polyphenols after simulated digestion.