Nitrogen (N) availability is the main constraint on primary production in most Arctic ecosystems, with microbial fixation of atmospheric N as the primary source of N input. However, there are only few reports on N fixation rates in relation to climate change in the Arctic. In order to investigate the effects of anticipated global climate change on N fixation rates in a subarctic moist heath, a field experiment was carried out in Northern Sweden. Warming was induced by plastic tents, and in order to simulate the effects of future increased tree cover, birch litter was added each fall for 9 years before the measurements. We analyzed N fixation rates on both whole-ecosystem level and specifically on two moss species: Sphagnum warnstorfii and Hylocomium splendens. The whole-ecosystem N fixation of the warmed plots almost tripled compared with the control plots. However, in the Sphagnum and Hylocomium mosses we observed either no change or occasionally even a decrease in N fixation after warming. Both measured on whole-ecosystem level and on the two moss species separately, litter addition increased N fixation rates. The results suggest that warming will lead to a general increased ecosystem N input, but also that the N fixation associated to some moss species is likely to decrease. Hence, this study shows that the scale of measurements is crucial when investigating on ecosystem responses to manipulations.