Betanin, a natural red pigment, is sensitive and prone to fading and discoloration, affecting its stability and bioavailability. Phytoferritin is a nano-diameter protein with unique interior-/exterior-interfaces. By the unique interfaces and pH-induced self-assembly of ferritin, a ferritin-betanin complex (FB) with an encapsulation efficiency of 17.66 ± 1.24% was prepared. The caffeic acid-FB (CFB) was further fabricated by attaching ferritin with caffeic acid, and the binding number n of caffeic acid was 88.47 ± 9.49, with a binding constant K of (1.63 ± 0.33) × 104 M-1. Fluorescence and Fourier transform infrared analysis indicated that the encapsulation of betanin and the binding of caffeic acid influenced the ferritin structure. The interaction between caffeic acid and ferritin was mainly through van der Waals forces and hydrogen bonds. TEM and DLS showed that the globular structure and diameter (12 nm) remained in CFB. Furthermore, the ferritin and caffeic acid exhibited a synergistic effect in enhancing thermal, light, and ferric ion stabilities, and controlled the betanin release in a more sustained manner in the simulated gastrointestinal tract. In addition, the antioxidant capacity of CFB was enhanced compared with free betanin. This study promotes the bioavailability of betanin by two interface-loading of ferritin, and guides the use of ferritin nanoparticles as a nanocarrier for pigment stabilization.