Summary Quinoa is considered as a superior gluten‐free material due to its balanced composition of amino acids in protein and abundant nutrients. However, the processing behaviour of quinoa flour is limited by protein functional properties. In this study, twin‐screw extrusion was used for the production of gluten‐free quinoa noodles (GFQNs). Moisture was found to be closely related to the cooking quality and texture characteristics of extruded noodles by regulating the formation of starch gel. With this in concern, the moisture dose was optimised as 30%. Then, soy protein isolate (SPI) was supplemented into quinoa flour to improve the texture and cooking quality of GFQNs while decrease its in vitro starch digestibility. It was found that SPI could significantly reduce the cooking loss of GFQNs from 16.65% to 11.82% while increase the hardness of the noodles from 6.35 N to 7.99 N, and form a more porous structure as observed by SEM. Furthermore, the addition of SPI also delayed the in vitro hydrolysis rate of quinoa‐based noodles, as shown by the significant decrease in rapid digestible starch around 8%. Therefore, quinoa–SPI mixture flour with the intermediate moisture extrusion showed prospective to develop low glycaemic index GFQNs.