In soil ecosystems, microorganisms exist in complex and diverse communities where microbial taxa are linked through different types of interactions. Therefore, pesticide application will not only directly affect certain microbial taxa, but will also have indirect effects throughout the community mediated through these interactions. These indirect effects may also influence ecosystem functions. In this study, a naturally occurring soil microbial community was fragmented by filtering a soil suspension and inoculating sterile soil microcosms. The effect of the fungicide Hymexazol on community structure and function was tested on the separate fractions and on the unfragmented community after a 40-day incubation period. We hypothesized that some taxa within the fragmented community would respond differently to pesticide application than in the unfragmented community, thereby unravelling indirect pesticide effects due to biotic interactions. Microbial communities were analyzed via high-throughput sequencing of 16S and 18S rRNA genes along with differential abundance and network analyses. We found that pesticide effects on microbial diversity vary between the different fractions and that fragmentation reveals pesticide effects that were not apparent in the unfragmented community. This work sheds light on ecological interactions between microbial taxa in soil and provides a novel approach for the development of procedures to assess pesticide toxicity at the ecosystem level.