<p>Extrusion cooking significantly alters the nutritional, digestive, and functional properties of pseudocereal flours. The high temperatures, shear forces, and pressure involved in the process induce substantial changes in macronutrient structures, enhancing digestibility and functional properties while mitigating the effects of certain anti-nutritional factors. Protein digestibility is influenced by denaturation and protein-starch interactions, while starch gelatinization and the breakdown of resistant starch improve starch digestibility. Simultaneously, the formation of starch-lipid and protein-starch complexes moderates enzymatic hydrolysis, promoting the development of slowly digestible and resistant starch fractions. These structural changes have direct implications for the glycemic index of pseudocereal-based foods. Although gelatinization may increase rapidly digestible starch and raise the glycemic index, the concurrent formation of resistant starch and lipid complexes can mitigate this effect, supporting improved glycemic control. The extent of these modifications is strongly influenced by extrusion parameters such as temperature, moisture content, and screw speed, highlighting the importance of process optimization. This review highlights the transformative role of extrusion in developing functional pseudocereal-based products tailored for enhanced nutritional quality and targeted health outcomes, such as improved protein bioavailability and glycemic management.</p>