Fungicides targeted at phytopathogens can be harmful to entomopathogenic fungi. The purpose of this study was to use ion-beam irradiation technology to produce benomyl-resistant mutants of the entomopathogenic fungus Beauveria bassiana (Bals.-Criv.) Vuill. After irradiation of conidia at 150 Gy, two mutant isolates, BB22 and BB24, were selected on media containing the fungicide. In an assay of vegetative growth, BB22 and BB24 were over 500 and 800 times more tolerant to benomyl, respectively, compared with the wild isolate. However, in an assay of conidial germination, neither mutant had increased tolerance compared with the wild isolate. Both mutant isolates also had increased tolerance to thiophanate-methyl during vegetative growth, but reduced tolerance to diethofencarb. A mutation was found at position 198 of the β-tubulin gene in the mutant isolates, with a substitution of glutamate for alanine (E198A). Ion beams have great potential as a tool to improve the traits of entomopathogenic fungi such as increasing tolerance to fungicides. Fungicide-resistant mutants produced in this way could be useful agents for biological control within IPM programmes where fungicides are also used.