SummaryDielectric barrier discharge atmospheric cold plasma (DBD‐ACP) treatment has been used to reduce microbial contamination on the surface of grains, contributing to improved food safety, however, its effect on the edible and processing of whole grain flours is not totally clear. In this study, the effect of DBD‐ACP (5 W, 0–20 min) on the nutritional, physicochemical and structural properties of whole quinoa (WQ), whole highland barley (WHB) and whole triticale (WT) were evaluated. Results showed that the effect of DBD‐ACP treatment on the nutrient composition of different flours differed between grain types. The total polyphenol content of WQ exhibited the most significant changes after 20 min of treatment, decreasing by 62.98%. In addition, DBD‐ACP treatment increased Thr, Phe and Tyr content and accelerated fat oxidation. The results of in vitro simulated digestion experiments indicated that DBD‐ACP treatment significantly reduced (P < 0.05) the final digestibility of three types of whole grain flours. Besides, 20 min of DBD‐ACP treatment significantly changed the physicochemical properties of samples, evidenced by improved hydration and pasting characteristics, increased water absorption index (WAI) and swelling power (SP) and reduced peak temperature (Tp) and gelatinisation enthalpy (∆Hg), especially in WQ20. Further structural analysis showed that DBD‐ACP treatment caused granule cross‐linking and reduced crystallinity of flours. In conclusion, this experiment provided a theoretical basis for the application of DBD‐ACP in grain processing.