Whole grain flour has captured increasing attention due to its health benefits. Herein, the quinoa flour-based composite gels were fabricated by heating quinoa flour dispersions containing 0-7 w/w% whey protein isolate (WPI). The thermal properties and gel formation of the dispersions were determined, along with the large deformation and fracture properties, microstructure, and molecular reorganization of the resulting gels. Protein hydrolysis, solid loss, glucose release and microstructural changes were monitored to characterize the gastrointestinal breakdown of the gels. Results showed that quinoa starch was gelatinized at 60-70 °C. Upon heating, quinoa starch was segregated into microparticles of ∼ 3 μm, which aggregated into the starch phase, whereas protein aggregates filled the gap of the starch gel network. A bicontinuous structure was formed with increasing WPI concentration to 7 w/w%. Meanwhile, the storage modulus, gel hardness and fracture stress of the gels increased by 5-8 times. The addition of WPI inhibited gel disintegration during in vitro digestion. However, intestinal glucose release was not delayed because of the phase-separated structure of the gels. With increasing WPI concentration, larger protein aggregates survived after 5 min of intestinal digestion, demonstrating that the enhanced protein network was the main contributor slowing down gel disintegration during in vitro digestion. This work would promote the development of quinoa flour-based products with controlled digestion.