AbstractPrevious studies demonstrated that a reduction in germination of Colletotrichum alienum conidia could be achieved following treatment with cold plasma (CP) or incubation with plasma‐activated water (PAW). In this study, the mode of action of CP and PAW on C. alienum conidia was explored using transmission electron microscopy. Following treatment of the conidia, noticeable ultrastructural changes were observed, including cell wall maceration, disorganization of the cytoplasm and vacuole, and changes to the nuclei and mitochondria. Disorganization of the cytoplasm was exhibited by 85% of conidia after CP or PAW treatment. Also, 85% of conidia were observed with disorganized vacuoles after 6 min of CP treatment and 65% after 3 hr incubation in PAW. Further, 45% or more conidia had modified cell walls after PAW incubation or CP treatment. Deformation of conidia was observed in 23% of conidia after PAW incubation. These ultrastructural changes are a likely reason for the reduced germination of C. alienum conidia following CP or PAW treatment.