Soy protein isolate (SPI) may serve as a health-enhancing functional ingredient in many food products due to the content of isoflavones. However, the high protein content may also be exploited as a structure modifier in gluten-free noodles. We applied Soy protein isolate to improve rice flour noodles’ structure, textural, and cooking properties by combining cross-linking and cold gelation of soy protein isolate using microbial transglutaminase and glucono-δ-lactone, respectively. The simultaneous cross-linking yielded noodles with improved structure and textural properties, mainly due to a more robust microstructure resulting from an increase in intermolecular protein cross-linking promoted by microbial transglutaminase and glucono-δ-lactone. However, the structurally enhanced noodles showed longer cooking time and reduced cooking yield upon drying. This was solved by employing pre-drying steaming treatments for 5 or 10 min to yield noodles with shorter cooking times, lower cooking losses, and improved cooking yield. We have also developed an alternative process technology using superheated steam (SHS) technology. The superheated steam technology made it possible to open up the structurally enhanced air-dried noodles by promoting faster gelatinization, as evidenced by reduced enthalpy, increased cooking yield, and sustained crystallinity of the starch granules noodle matrix.