Biopurification systems (BPS) have been introduced to minimise the risk for point source contamination of natural water resources by pesticides. Their depuration efficiency relies mostly on the high biodegradation of their packing substrate (biomixture). Despite that, little is known regarding the interactions between biomixture microflora and pesticides, especially fungicides which are expected to have a higher impact on the microbial community. This study reports the dissipation of the fungicides azoxystrobin (AZX), fludioxonil (FL) and penconazole (PC), commonly used in vineyards, in a biomixture composed of pruning residues and straw used in vineyard BPS. The impact of fungicides on the microbial community was also studied via microbial biomass carbon, basal respiration and phospholipid fatty acid analysis. AZX dissipated faster (t1/2 = 30.1 days) than PC (t1/2 = 99.0 days) and FL (t1/2 = 115.5 days). Fungicides differently affected the microbial community. PC showed the highest adverse effect on both the size and the activity of the biomixture microflora. A significant change in the structure of the microbial community was noted for PC and FL, and it was attributed to a rapid inhibition of the fungal fraction while bacteria showed a delayed response which was attributed to indirect effects by the late proliferation of fungi. All effects observed were transitory and a full recovery of microbial indices was observed 60 days post-application. Overall, no clear link between pesticide persistence and microbial responses was observed stressing the complex nature of interactions between pesticides in microflora in BPS.