There is almost no information on how restoration of Sphagnum-dominated peatbogs, and in particular removal of reeds, affects the functioning of ciliate communities. Changes in vegetation patterns caused by restoration procedures may take years to be observed, while microbial processes already display effects after short-term exposure to changes in environmental conditions due to restoration. Based on the results of a long-term study, we assumed that mowing down of reeds causes changes in the physicochemical properties of peatbog water and sought to answer the question of how ciliate communities react to these changes and whether these microorganisms can play a significant role as bioindicators in evaluating the restoration process. Removal of reeds clearly modified the taxonomic composition and abundance of ciliates. This was reflected in an increase in the abundance and diversity of these protozoa and in a significant increase in the proportion of sphagnophilous species. Our results suggest an indicator species approach based on functional groups may be appropriate for biomonitoring peatbog restoration. A better understanding of what regulates microbial populations and activity in peatbogs and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how peatbogs will respond to anthropogenic disturbances.