This research aimed to prepare quinoa protein isolate (QPI) based nanocomposite films reinforced with starch and cellulose nanocrystals (CNC). The range of QPI, starch, and CNC contents were chosen as 60%–80%, 10%–30%, and 2.5%–7%, respectively, by mixture design approach. The effect of CNC and starch on physicochemical, mechanical, and barrier properties of the films were then investigated. The obtained results showed that the addition of starch and CNC improved the mechanical properties of films. The incorporation of CNC reduced the film water vapor permeability (WVP). In addition, transparency of the films increased with increasing protein and starch content and reducing CNC content. Furthermore, the optimal formulation of the composite was determined as 78.55% protein, 18.28% starch, and 3.17% CNC. Fourier transform infrared (FTIR) spectroscopy of the film prepared according to optimal formulation demonstrated the interaction of the film's constituents, and its scanning electric spectroscopy (SEM) image was in agreement with the physical and mechanical properties the nanocomposite film. Novelty impact statement Protein extracted from quinoa seeds using alkaline method with high purity (83%). The optimal formulation obtained with 78.55% protein, 18.28% starch, and 3.17% CNC. The optimal film is recommended for packaging of aromatic foodstuff.