To improve the physicochemical stability of hydrophobic flavonoids, a series of protein-based nanomicelles have been developed in recent years. However, the quinoa protein (QP) nanomicelles and its interactions with different flavonoids were rarely reported. In this study, the QP nanomicelles (48.6 nm) were initially prepared. Then, quercetin (Que), curcumin (Cur), luteolin (Lut) and resveratrol (Res) were successfully assembled into the hydrophobic region of QP nanomicelles, giving the loading capacity of 33.9%, 8.0%, 17.8% and 6.4%, respectively. Moreover, this self-assembly significantly enhanced the solubility and stability of four flavonoids. The molecular interactions were further investigated. Results showed that hydrophobic interaction and hydrogen bonding were the main interaction driving forces between QP and hydrophobic flavonoids. The present work provided valuable evidences for the application of quinoa protein in functional foods. Display omitted •Quinoa protein (QP) was extracted from quinoa seeds.•Hydrophobic flavonoids were successfully assembled in QP nanomicelles.•Flavonoids inducing the fluorescence quenching of QP via self-assembly.•Hydrophobic interaction and hydrogen bonding were the main molecular driving forces.