Nitrogen pollution affects many peatlands with consequences for their biodiversity and ecosystem function. Microorganisms control nutrient cycling and constitute most of the biodiversity of peatlands but their response to nitrogen is poorly characterised and likely to depend on the form of deposition. Using a unique field experiment we show that ammonia exposure at realistic point source levels is associated with a general shift from heterotrophic (bacteria and fungi) to autotrophic (algal) dominance and an increase in total biomass. The biomass of larger testate amoebae increased, suggesting increased food supply for microbial predators. Results show the widespread impacts of N pollution and suggest the potential for microbial community-based bioindicators in these ecosystems.