Mycorrhizal fungi can contribute to soil carbon sequestration by immobilizing carbon in living fungal tissues and by producing recalcitrant compounds that remain in the soil following fungal senescence. We hypothesized that nitrogen (N) fertilization would decrease these carbon stocks, because plants should reduce investment of carbon in mycorrhizal fungi when N availability is high. We measured the abundance of two major groups of mycorrhizal fungi, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, in the top 10 cm of soil in control and N-fertilized plots within three Alaskan boreal ecosystems that represented different recovery stages following severe fire. Pools of mycorrhizal carbon included root-associated AM and ECM structures; soil-associated AM hyphae; and glomalin, a glycoprotein produced by AM fungi. Total mycorrhizal carbon pools decreased by approximately 50 g C m−2 in the youngest site under N fertilization, and this reduction was driven mostly by glomalin. Total mycorrhizal carbon did not change significantly in the other sites. Root-associated AM structures were more abundant under N fertilization across all sites, and root-associated ECM structures increased marginally significantly. We found no significant N effects on AM hyphae. Carbon sequestered within living mycorrhizal structures (0.051–0.21 g m−2) was modest compared with that of glomalin (33–203 g m−2). We conclude that our hypothesis was only supported in relation to glomalin stocks within one of the three study sites. As N effects on glomalin were inconsistent among sites, an understanding of the mechanisms underlying this variation would improve our ability to predict ecosystem feedbacks to global change.