Wheat kernels harbor a diverse microflora that can negatively affect the suitability of the grains for further processing. To reduce surface microflora, a kernel disinfection method is required that does not affect grain functionality. Three different versions of gas phase hydroxyl‐radical processes were compared with the common method for grain disinfection, that is, a bleach treatment. The gas phase hydroxyl‐radicals are generated by the UV‐C mediated degradation of hydrogen peroxide and/or ozone in a near water‐free process. It was found that treating kernels with a bleach solution could reduce total aerobic count (TAC) and fungal count to below the level of enumeration. In comparison, the gas phase hydroxyl‐radical treatment, that is, H2O2–UV–ozone treatment, could support a 1.3 log count reduction (LCR) in TAC and a 1.1 LCR in fungal count. The microbial load reduction for the wholemeal samples was less pronounced as endophytic microorganisms were less affected by all treatments, hinting at a limited penetration depth of the treatments. Despite reducing the microbial load on the kernel surface through the bleach and H2O2–UV–ozone treatments, none of these treatments resulted in a reduced microbial count on grains that underwent sprouting after the treatments. No negative effect on germination power or development of the seedling was observed for any of the treatments. The gluten aggregation behavior and xylanase activity of the wholemeal also remained unchanged after the gas phase hydroxyl‐radical treatments. Our findings suggest that UV–H2O2–ozone treatment shows promise for dry‐kernel disinfection, but further optimization of the processing parameters is required.