For centuries European peatlands have been degrading along with drainage, land use and climate changes. Increasing pressure on peatland ecosystems calls for a more cost-efficient method to indicate the current state of peatlands and the success of restoration efforts. Metabolic pathways in peatland soils are imprinted in stable isotope compositions due to differences in microorganism communities and their metabolic pathways. Therefore, we hypothesize that depth profiles of nitrogen stable isotope values provide a promising opportunity to detect peatland decomposition or restoration. We studied five peatlands, namely Degerö Stormyr (northern Sweden), Lakkasuo (central Finland) and three mires in the Black Forest (southern Germany). At all locations, cores were taken from adjacent drained (or rewetted) and natural sites to identify δ 15N trends that could indicate changes due to drainage and restoration. At all drained (and rewetted) sites we found a distinct peak (“turning point”) of the δ 15N values in the center of the drained horizon. We did a fatty acids (FAs) analysis to link our results to microbial community composition. As markers, we distinguished between one fungal-derived FA (C18:2ω9c) and four bacterial-derived FAs. For bacteria, we looked for one general bacterial-derived FA (C14:0), two FAs for gram-positive bacteria (i-C15:0; a-C15:0), and one FA for gram-negative bacteria (C16:1ω9c). In accordance with other studies, our results suggest that fungi dominate the microbial metabolism in the upper aerobic peat horizon. This is reflected by depleted δ 15N values. Moving downwards, the drained horizon conditions slowly switch to oxygen limitation. Consequently, fungal-derived FAs decrease whereas bacterial-derived FAs rise. The highest diversity of microbial-derived FAs is indicated by the δ 15N turning point. Below the δ 15N turning point, oxygen is increasingly limited and concentrations of all microbial-derived FAs are decreasing down to the onset of the permanently waterlogged anaerobic horizon. Peatland cores with restoration successes again show, above the formerly drained horizon, no depth trend of the isotopic values. Hence, we conclude that δ 15N stable isotope values reflect microbial community composition, which differs between drained and natural peatlands.