Colored rice anthocyanins are water-soluble natural pigments that can be used as an active ingredient in healthy food and pharmaceutical products. However, anthocyanin utilization is limited because of its instability. This work produced anthocyanin-rich gel beads from colored rice using a modified ionotropic gelation technique for encapsulation, and their efficacy was studied in vitro in the gastrointestinal tract. In total, 15 colored rice samples of three types (whole grain rice, ground rice, and ground germinated rice) were screened to identify the highest anthocyanin content. The anthocyanin content of the whole grain rice was significantly (p < 0.05) higher than it was in the ground and ground germinated rice. The sample with the highest anthocyanin content (1062.7 µg/g) was the black glutinous rice grain from Phrae, chosen based on its anthocyanin-rich crude extract. A new formula using a modified ionotropic gelation technique was prepared for the inclusion of the extract in gel beads. The results indicated that the incorporation of oil and wax significantly increased the encapsulation efficiency of the gel beads (% EE value of 85.43%) and improved the bioavailability of the active ingredient. Moreover, after simulated digestion, the release of anthocyanin and total phenolic content occurred more than five times. Scanning electron microscopy revealed that the surface of the gel beads was smooth. Furthermore, the presence of polyphenols and polysaccharides in the gel beads was confirmed using FTIR. The oil-wax-incorporated, anthocyanin-rich gel beads could be implemented for antioxidant delivery into the gastrointestinal tract to further improve healthy food and nutraceutical products.