Cyanobacteria periodically dominate phytoplankton composition in lakes, and produce a wide array of toxic secondary metabolites. Blooms of cyanobacteria often coincide with infections of zooplankton by microparasites (such as Metschnikowia bicuspidata, a parasitic yeast of Daphnia), and prior research has shown that cyanobacteria-based diets could mitigate fungal infections of the host. Here, we tested whether cyanotoxins could exert detrimental effects against free-living parasite stages: we inoculated two genotypes of the host Daphnia galeata × longispina with fungal spores, which were previously exposed to cyanobacterial extracts or to a placebo solution. Additionally, to test for interactive effects of cyanotoxins through environmental exposure and host consumption, Daphnia from each treatment were fed using either green algae or the same cyanobacterium. Exposing spores to cyanobacterial extracts did not reduce their infectivity; instead, parasite infectivity was increased, but only on one host genotype. The effect of host diet on parasite growth was also host-genotype dependent, with only one Daphnia genotype showing impaired spore production under a toxic diet. Our results suggest that dissolved cyanobacterial compounds released during blooms may not exert any detrimental effect on fungal spore banks, but likely influence transmission of the parasite when incorporated as part of the host’s diet.