Abstract This study examines the recovery of the microbial compartment following active restoration of a North American ombrotrophic peatland extracted for horticultural peat-based substrates and restored by the Sphagnum moss transfer method. We used phospholipid fatty acids (PLFAs) to portrait the microbial community structure and Community Level Physiological Profiles (CLPP) to describe the functional diversity of the microbial communities. Our results indicate that the PLFA profiles were different between the beginning and the end of the growing season, but that it was impossible to distinguish five different vegetation classes found along the disturbance-recovery gradient on the basis of the microbial community structure. The pH, the cover of mosses, Ledum groenlandicum and Eriophorum vaginatum var. spissum were the best environmental predictors for the PLFA composition. The newly formed peat found in aerobic conditions beneath restored Sphagnum carpets had the highest decomposition capacity, whereas the lowest rates were found in the surface samples of non-restored conditions or in the deepest horizons of the natural samples. A large proportion of the variation in the physiological profiles was explained with variables related to the vegetation cover, the physicochemical environment and the microbial structure of the community, which is very promising for future monitoring studies. Overall, this study demonstrates that the recovery of particular plant groups, namely mosses and shrubs in restored peatlands might be the driver of changes occurring in the structure of the microbial communities in restored peatlands.