Quinoa, known for its nutritional quality and as a low GI food, has arose great interests of scientists in the recent past. Intrinsic properties of starch as well as endogenous proteins and lipids might be important factors influencing the digestion processes of cooked quinoas. This work aims to investigate the roles of endogenous proteins and lipids on starch digestibility in the quinoa flour, and uncover the physicochemical and textural properties related to the digestion process. Quinoa flours with/without proteins and/or lipids removal were obtained and then subjected to an in vitro digestion before/after cooking. Interestingly, the cooked whole quinoa flours had the highest starch digestibility and eGI, followed by the flours with protein or lipid removal, with the smallest digestibility found in the pure quinoa starch. This was in an opposite order of the equivalent raw quinoa flours, where proteins and lipids strongly inhibit the starch digestion. The cooked whole quinoa flours showed a first-order kinetic digestion pattern, with continuous hydrolysis of the long amylose chains, compared to combination of parallel and sequential digestion kinetic observed for other quinoa samples and the reduction in amylopectin with DP ∼20–250 noted during the fast digestion stage. Additionally, compared to whole quinoa flours, samples with protein and/or lipid removal displayed the higher final viscosity and shear-thinning property, with aggregated starch observed under confocal laser scanning microscopy. It suggested that gel network is a primary factor affecting the digestion process of starch in different quinoa flours. Ultimately, this work provides new insights for the development and processing of healthy quinoa products. • Whole quinoa flours had the highest starch digestibility and eGI. • The cooked whole quinoa flours showed a first-order kinetic digestion pattern. • Samples with protein and lipid removal displayed higher final viscosity. • Aggregated starch observed under confocal laser scanning microscopy. • Gel network is potentially a primary factor affecting the digestion process.