Interactions between microbial communities and the classical grazing food chain are essential for understanding the functioning of peatbog ecosystems. However, little is known of how short-term intensification of eutrophication processes may influence microbial and metazoan communities in transitional peatbog. We addressed the hypothesis that an increase in the concentration of nutrients will affect the species richness and abundance of microorganisms and small metazoans and cause changes in the food web structure in a peatbog. The experiments were performed in a transitional peatbog. Four experimental variants were conducted (control and nutrient-enriched: +P, +N and P+N). Increased habitat fertility was found to modify the taxonomic composition and functioning of microbial communities. We observed a strong reduction in the species richness of testate amoebae-top predators, and a substantial increase in the abundance of bacteria, flagellates and ciliates. A better understanding of which parameters regulate microbial populations in peatbogs is critical for more accurate prediction of how peatbogs will respond to global climate change or anthropogenic disturbances.