Presently, there is uncertainty regarding the degree to which anthropogenic N deposition will foster C storage in the N-limited forests of the Northern Hemisphere, ecosystems which are globally important sinks for anthropogenic CO2. We constructed organic matter and N budgets for replicate northern hardwood stands (n = 4) that have received ambient (0.7–1.2 g N·m-2·yr-1) and experimental NO3- deposition (ambient plus 3 g NO3–N·m-2·yr-1) for a decade; we also traced the flow of a 15NO3- pulse over a six-year period. Experimental NO3- deposition had no effect on organic matter or N stored in the standing forest overstory, but it did significantly increase the N concentration (+19%) and N content (+24%) of canopy leaves. In contrast, a decade of experimental NO3- deposition significantly increased amounts of organic matter (+12%) and N (+9%) in forest floor and mineral soil, despite no increase in detritus production. A greater forest floor (Oe/a) mass under experimental NO3- deposition resulted from slower decomposition, which is consistent with previously reported declines in lignolytic activity by microbial communities exposed to experimental NO3- deposition. Tracing 15NO3- revealed that N accumulated in soil organic matter by first flowing through soil microorganisms and plants, and that the shedding of 15N-labeled leaf litter enriched soil organic matter over a six-year duration. Our results demonstrate that atmospheric NO3- deposition exerts a direct and negative effect on microbial activity in this forest ecosystem, slowing the decomposition of aboveground litter and leading to the accumulation of forest floor and soil organic matter. To the best of our knowledge, this mechanism is not represented in the majority of simulation models predicting the influence of anthropogenic N deposition on ecosystem C storage in northern forests.