Anthocyanins have antioxidant, anti-inflammatory, and anticancer properties but have limited bioaccessibility and bioavailability due to molecular instability in the gastrointestinal tract. This study evaluated the absorption and biodistribution of free and nanoencapsulated radiolabeled anthocyanin (cyanidin-3-O-glucoside). A new methodology was efficiently developed for radiolabeling anthocyanins with Technetium (99mTc-anthocyanins). Then, the anthocyanins were nanoencapsulated through self-assembly using citrus pectin and lysozyme. The nanostructures have a size of 190 nm, a zeta potential of –30 mV, and an invariably spherical and homogeneous morphology. The biodistribution in different tissues, the kinetics of absorption, and molecular visualization by micro single-photon emission computed tomography/computed tomography (µSPECT/CT) showed that the nanoencapsulated anthocyanins are absorbed differently than free anthocyanin in mice. After oral administration, nanostructured anthocyanins were delivered to the blood, spleen, bladder, pancreas, and bone, unlike unencapsulated anthocyanins found only in kidneys and bladder. In silico data indicated the stabilization between compounds in nanocapsules and demonstrated the pH-dependent release of anthocyanins in the intestine. The nanoencapsulation alters the absorption kinetics, increasing the blood’s bioavailability and the organs’ uptake, suggesting an improvement of the biological effects and potential clinical application.