Isaria fumosorosea and Isaria farinosa are important entomopathogenic fungi with a worldwide distribution and multiple host insects. However, the concerns about the safety risks of myco-pesticides have been attracting the attention of researchers and consumers. Secondary metabolites (SMs), especially the mycotoxins, closely affect the biosafety of Isaria myco-insecticides. In the last forty years, more than seventy SMs were identified and isolated from I. fumosorosea and I. farinose. The SMs of I. fumosorosea include the mycotoxins of non-ribosomal peptides (NRPs) (beauvericin and beauverolides), terpenes (trichocaranes and fumosorinone), lactone compounds (cepharosporolides), acids (dipicolinic acid and oxalic acid), etc. Meanwhile, the NRP mycotoxins (cycloaspeptides) and the terpene compounds (farinosones and militarinones) are the main SMs in I. farinosa. Although several researches reported the two Isaria have promised biosafety, the bioactivities and the safety risks of their SMs have not been studied in detail so far. However, based on existing knowledge, most SMs (i.e., mycotoxins) do not come from Isaria myco-insecticide itself, but are from the host insects infected by Isaria fungi, because only the hosts can provide the conditions for fungal proliferation. Furthermore, the SMs from Isaria fungi have a very limited possibility of entering into environments because many SMs are decomposed in insect cadavers. The biosafety of Isaria myco-insecticides and their SMs/mycotoxins are being monitored. Of course, SMs safety risks of Isaria myco-insecticides need further research.