The low solubility, instability, and low bioavailability of food bioactive compounds such as polyphenols and flavonoids, restrict their applications in the fields of food science and nutrition. Ferritin protein has received more and more attention in encapsulation and delivery of the bioactive compounds due to its nanosized shell-like structure and its reversible self-assembly character. After encapsulation, bioactive compounds can be functionalized by the ferritin vehicle to achieve stabilization, solubilization, and targeted delivery. In addition, the outer interfaces and the porous structure of ferritin are also artfully harnessed for encapsulation. This review focuses on the newest advances in the fabrication, characterization, and application of ferritin-based nano-carriers for bioactive compounds by the reversible self-assembly, outer-interface decoration methods, and the channel-directed approach. The functional improvements of food bioactive compounds, including their solubility, stability, and cellular uptake, are emphasized. The limitations that affect ferritin encapsulation are also examined.