BACKGROUND Commercial formulations based on Bacillus thuringiensis subs. kurstaki (Btk) and Beauveria bassiana (Bb) are commonly used microbial insecticides in Brazil and other tropical regions. However, and despite being considered environmentally friendly, their use generates concerns regarding possible adverse ecological effects in freshwater ecosystems. Here, we evaluate the effects of these bioinsecticides on the tropical aquatic dipteran Chironomus xanthus under laboratory conditions. RESULTS After laboratory exposures to these compounds 48‐h median lethal concentration (LC50) values of 1534 μg a.i./L for Btk and of 6.35 μg a.i./L for Bb were estimated. Chronic assays revealed different sublethal effects: Btk‐based bioinsecticide exposure reduced C. xanthus growth [lowest observed effect concentration (LOEC) was 126 μg a.i./L for head width], decreased emergence rate (LOEC = 8 μg a.i./L) and increased immunological response (LOEC = 50 μg a.i./L) measured as total hemocyte count in larvae hemolymph. Exposure to low concentrations of Bb‐based insecticide also reduced C. xanthus growth (LOEC = 0.07 μg a.i./L for larvae body length measurements), and emergence rate (LOEC = 0.28 μg a.i./L), despite no clear effects on the total hemocyte counts. CONCLUSION Our results suggest that low concentrations of Btk and Bb bioinsecticides are toxic to C. xanthus. Given their widespread use and occurrence in tropical freshwater systems, research is needed to evaluate the potential effects of these compounds concerning natural freshwater insect communities and ecosystem functioning. © 2019 Society of Chemical Industry