Enrichment of multiple bioactive components with different characters into one food substrate simultaneously is a challenge. In this study, the hydrophilic epigallocatechin gallate (EGCG) and the hydrophobic quercetin were simultaneously enriched in the cavity of phytoferritin from red bean seed deprived of iron (apoRBF), a cagelike protein. The interactions of apoRBF with EGCG and quercetin were evaluated by UV/visible absorption, fluorescence, and circular dichroism technologies. By combination of the reversible assembly and urea induced approaches, both EGCG and quercetin were successfully coencapsulated in apoRBF to fabricate four kinds of apoRBF-EGCG-quercetin nanocomplexes FEQ (FEQ1, FEQ2, FEQ3, and FEQ4) with good solubility in aqueous solution. All FEQ samples maintained the typically spherical morphology of ferritin cage with a diameter around 12 nm. Among the four FEQ samples, the FEQ1 prepared by involving a pH 2.0/6.7 transition scheme was more effective in encapsulating EGCG and quercetin molecules than that by the urea induced method. Furthermore, all FEQs facilitated the stability of EGCG and quercetin molecules relative to free ones, and simultaneous coencapsulation of EGCG and quercetin could significantly improve the quercetin stability as compared with that of the free one and quercetin-loaded ferritin (p < 0.05), respectively. This work provides a new scheme to design and fabricate the ferritin based carrier for encapsulation of multiple bioactive components, and it is beneficial for the intensification of multifunction in one food substrate.