Fungi are the leading cause of plant diseases worldwide and are responsible for enormous agricultural and industrial losses on a global scale. Cold plasma (CP) is a potential tool for eliminating or inactivating fungal contaminants from biological material such as seeds and grains. This study used a low-pressure radiofrequency CP system with oxygen as the feed gas to test the decontamination efficacy of different genera and species commonly colonising buckwheat grains. Two widely accepted methods for evaluating fungal decontamination after CP treatment of seeds were compared: direct cultivation technique or contamination rate method (%) and indirect cultivation or colony-forming units (CFU) method. For most of the tested fungal taxa, an efficient decrease in contamination levels with increasing CP treatment time was observed.Fusarium graminearumwas the most susceptible to CP treatment, whileFusarium fujikuroiseems to be the most resistant. The observed doses of oxygen atoms needed for 1-log reduction range from 1024–1025m−2. Although there was some minor discrepancy between the results obtained from both tested methods (especially in the case ofFusariumspp.), the trends were similar. The results indicate that the main factors affecting decontamination efficiency are spore shape, size, and colouration.