Nitrogen (N) deposition has increased soil carbon (C) storage across eastern US temperate forests by reducing microbial decomposition. However, the fate of these N-induced soil C gains are uncertain given strong declines in N-deposition rates and rising soil temperatures. As N deposition has reduced soil pH and plant C investments into the rhizosphere, we compared the extent to which removing limitations to microbial decomposition by increasing soil pH, adding artificial root exudates, or elevating soil temperature would increase microbial decomposition in soils that have and have not received excess N inputs. We hypothesized that alleviating these microbial decomposition limitations would prime soil C losses from soils that have received excess N inputs. To test this hypothesis, we conducted a soil microcosm experiment where we compared microbial respiration, microbial biomass, and soil enzyme activity in soils from an unfertilized watershed and a previously N-fertilized watershed 4 years after the end of a 30-year N deposition experiment at the Fernow Experimental Forest in West Virginia. In both watersheds, we found that removing pH, plant carbon, or temperature limitations to decomposition stimulated microbial respiration. However, microbial decomposition and soil C losses were consistently lower in the previously N-fertilized watershed across all treatments. This response, coupled with a lack of differences in microbial biomass between watersheds and treatments, suggests that long-term N fertilization has fundamentally altered soil microbial communities and has led to a sustained impairment of the ability of the microbial community to decompose soil organic matter. Collectively, our results indicate that the legacy effect of N deposition on microbial communities may influence the persistence of soil C stocks in the face of global change.