Organic peat soils have been extensively drained and used for agricultural, horticultural and energy purposes. The management practices of organic soils accelerate decomposition processes resulting generally in loss of carbon. Microbes are the key players in soil carbon cycling. We studied the effects of cultivation of a perennial bioenergy plant (reed canary grass, Phalaris arundinacea) on microbial biomass carbon, microbial respiration and microbial communities in an old, previously uncultivated peat soil. The cultivation increased the amount of microbial biomass carbon and microbial respiration in peat mostly in the uppermost 5 cm layer where the impacts of roots and litter are most pronounced. As shown by phospholipid fatty acid (PLFA) analysis, the abundance of fungi and gram-negative bacteria increased with cultivation, while the abundance of gram-positive bacteria decreased. The implications of these changes on carbon cycling and carbon storage in peat under reed canary grass are discussed.