Electron beam (EB) irradiation was tested to determine the dose required to eradicate plant pathogens, such as Botrytis cinerea and Agrobacterium rhizogenes, from the infected seeds without affecting the germination rate of the irradiated vegetable seeds, including crown daisy, cucumber, hot pepper, green onion, leaf lettuce, and radish seeds. EB irradiation of 1.5 kGy and 2 kGy was sufficient to kill 100% of hairy root disease bacteria and gray mold conidia, respectively. EB irradiation showed no effect or minimal effect on the germination rate of the crown daisy, cucumber, green onion, and radish seeds. However, the germination rate of the hot pepper and leaf lettuce seeds was significantly reduced by using 2 kGy of EB irradiation. Difference in susceptibility to EB irradiation appears not to be related to the weight of each seed, but to the intrinsic characteristic of each plant. Conclusively, EB irradiation might be a useful way to decontaminate crown daisy, cucumber, green onion, and radish seeds.