Soybean aphid, Aphis glycines Matsumura, is a serious pest of soybean in North America and now that Asian soybean rust has arrived, fungicide use is expected to increase, possibly having a detrimental effect on beneficial fungi that are important regulators of soybean aphid population growth. In 2007, field plots composed of R2 soybeans were treated with a strobilurin fungicide, a strobilurin-triazole mix, or water (control) either before (time 1) or after (time 2) the artificial initiation of a Pandora neoaphidis epizootic. The entire experiment was repeated when soybeans reached R5. Pandora neoaphidis establishment was reduced in fungicide-treated plots when compared to control plots and this difference was strongest in the plots treated with the strobilurin-triazole mix at time 1, where infected aphids were recovered in only 33% of plots, compared to 100% of corresponding control plots. Disease prevalence was monitored throughout the epizootics. In the first run, the mean percent prevalence of disease in plots treated with fungicide at time 1 was reduced to 21% and 17% of the water-treated control for the strobilurin and strobilurin-triazole mix, respectively. During the second run, environmental conditions became exceptionally beneficial for disease transmission limiting the treatment effects. These results confirm previous studies and demonstrate that fungicide applications will negatively impact disease prevalence of P. neoaphidis; however, environmental conditions can mitigate the negative impacts in extreme cases. Further, applications made prior to epizootic initiation seem to limit the ability of the disease to establish in an aphid population.