Anthocyanins are flavonoids with reported chemoprotective activities in the oral cavity. However, information about their stability, metabolism, and tissue uptake in the mouth is limited. Anthocyanin chemical structure was recently shown to affect their stability ex vivo in saliva, and it was hypothesized that structure may affect their availability in oral tissues in vivo. Here, 12 healthy individuals retained red grape or chokeberry juice in the mouth for 5 min. Anthocyanin stability, mucus binding, and uptake into epithelial cells were evaluated. Loss of delphinidin-3-glucoside in red grape juice exceeded that of other anthocyanin-glucosides, and lesser amounts of delphinidin- and petunidin-glucosides were associated with buccal scraping, suggesting the loss was due to degradation. In chokeberry juice, loss of cyanidin-3-xyloside exceeded that of other anthocyanins, whereas cyanidin-3-glucoside preferentially accumulated in epithelium cells. These results suggest that anthocyanin structure affects stability and buccal cell uptake and therefore the potential efficacy of anthocyanin-rich products for the promotion of oral health.