BACKGROUND: Quinoa (Chenopodium quinoa Willd.) flour and processed traditional Peruvian quinoa breakfast foods were studied to evaluate the effect of extrusion and post-processing on protein properties, morphology and nutritional characteristics (amino acids and dietary fibers). RESULTS: The extrusion increased quinoa protein crosslinking and aggregation observed by size exclusion high-performance liquid chromatography and the amount of soluble fibers, as well as decreasing the amounts of insoluble fibers in the processed foods. The post-processing drying resulted in additional crosslinking of large protein fractions in the quinoa products. The microstructure of the extruded quinoa breakfast flakes and heat-post-processed samples studied by scanning electron microscopy and X-ray tomography differed greatly; post-drying induced formation of aerated protein microstructures in the heat-treated samples. Nanostructures revealed by small-angle and wide-angle X-ray scattering indicated that extrusion imparted morphological changes in the quinoa protein and starch (dominance of V-type). Overall, extrusion processing only reduced the content of most of the essential amino acids to a minor extent; the content of valine and methionine was reduced to a slightly greater extent, but the final products met the requirements of the Food and Drug Organization. CONCLUSION: This study presents innovative examples on how extrusion processing and post-processing heat treatment can be used to produce attractive future food alternatives, such as breakfast cereal flakes and porridge powder, from quinoa grains. Extrusion of quinoa flour into Peruvian foods was shown to be mostly impacted by the processing temperature and processing conditions used. Protein crosslinking increased due to extrusion and post-processing heating. Starch crystallinity decreased most when the product was dried after processing. © 2021 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.