Cold plasma is an emerging technology to improve microbiological safety as well as functionality of foods. This study compared the effect of radio frequency cold plasma on flour and dough properties of three members of the Triticeae tribe, soft as well as hard wheat (Triticum aestivum L.) and intermediate wheatgrass (Thinopyrum intermedium, IWG). These three flour types differ in their protein content and composition and were evaluated for their solubility, solvent retention capacity, starch damage, GlutoPeak and Farinograph profiles, and protein secondary structures. Plasma treatment resulted in dehydration of flours but did not change protein content or solubility. Farinograph water absorption increased for all flours after plasma treatment (from 56.5–61.1 before to 71.0–81.6%) and coincided with higher solvent retention capacity for water and sodium carbonate. Plasma treatment under our conditions was found to cause starch damage to the extent of 3.46–6.62% in all samples, explaining the higher solvent retention capacity for sodium carbonate. However, Farinograph properties were changed differently in each flour type: dough development time and stability time decreased for hard wheat and increased for soft wheat but remained unchanged in intermediate wheatgrass. GlutoPeak parameters were also affected differently: peak torque for intermediate wheatgrass increased from 32 to 39.5 GlutoPeak units but was not different for the other two flours. Soft wheat did not always aggregate after plasma treatment, i.e., did not aggregate within the measurement time. It was also the only flour where protein secondary structures were changed after plasma treatment, exhibiting an increase from 15.2 to 27.9% in β-turns and a decrease from 59.4 to 47.9% in β-sheets. While this could be indicative of a better hydrated gluten network, plasma-treated soft wheat was the only flour where viscoelastic properties were changed and extensibility decreased. Further research is warranted to elucidate molecular changes underlying these effects.