Non‐infected and infected cereal crops, respectively, are treated in the afterglow of Ar/N2‐O2 surface‐wave microwave discharges at 2–8 mbar pressure. It is shown, that the germination and vigour of non‐infected seeds are not significantly effected, when barley is treated max 120 s at 2 mbar and maize 240 s at 4 mbar. On the other hand, seeds can be disinfected from the germination inhibitors Fusarium graminearum and Fusarium verticillioides. The most efficient treatment, which also increases the germination of infected seeds above 80%, for barley is the 3 min Ar‐20%O2 afterglow at 4 mbar, while for maize the 4 min Ar‐20%O2 + 2 min N2‐2%O2 at 8 mbar. The high NO content mixtures and the heating of seed surface by the recombination of O and N‐atoms inhibit barley germination.