The objective of this work was to generate and characterize complexes of quinoa proteins (QP) with either resveratrol (RSV) or tocopherol (TOC) whose dimensions fell into the nanoscale. The QP-based nanocomplexes characterization was carried out jointly with encapsulation efficiency determination. Fourier-Transform Infrared Spectroscopy (FTIR) showed no covalent bond formation and indicated that the protein’s secondary structure was modified. Transmission Electron Microscopy (TEM) images and Dynamic Light Scattering (DLS) measurements confirmed that the addition of bioactive compounds did not substantially alter the protein’s original size. A consistent particle diameter of 100 nm was observed in both types of nanocomplexes with and without RSV and TOC. The antioxidant capacity of nanocomplexes was analyzed after an in vitro simulated digestion process, showing an increase in this property post-digestion. These nanocomplexes hold great potential as functional ingredients.