Many studies have used Caco-2 cell monolayers as human intestinal absorption models. However, only a few studied digested foods, instead of pure standard compounds. Moreover, beneficial and nutritional molecules (nutriome) have not been investigated simultaneously. The present study explored nutriome passages from digest solution of fresh, dried, and juiced tomato, mango, and papaya using Caco-2 cell monolayers in apical→basolateral directions. A validation method using complementary TEER and P_app values or internal standard caffeine is recommended because physiologically passive diffusion is unlikely to happen. Sugars were transported into basolateral sides, resulting in potential glucose equivalent bioavailability of 2.26−75 mg h⁻¹/100 g (WB). Using sugar passage rates (DB) of juices as 100% references, the rate order was tomato (49.8% dried; 89.5% fresh) > mango (56.8% dried; 22.8% fresh) > papaya (18.7% dried; 36.7% fresh). Major indications that phytochemical absorption does not occur in the small intestine were obtained from the bioassay condition selected. Apical organic acid levels decreased, which occasionally were transported into basolateral sides, whereas the disappearances of apical carotenoids and phenolics were not. Pectin substances were predicted to be responsible for the disappearances of bioactive compounds in those pectin-rich fruits. Further investigations on the role of pectin substances in intestinal passages are recommended.