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Vegetation changes in a warming Arctic may affect plant-associated soil microbial communities with possible consequences for the biogeochemical cycling of carbon (C) and nitrogen (N). In a sub-arctic tundra heath, we factorially removed plant species with ecto- and ericoid mycorrhizal associations. After two years, we explored how mycorrhizal type-specific plant removal influences microbial communities, soil and microbial C and N pools, and extracellular enzymatic activities. Removal of ecto- and ericoid mycorrhizal plants did not change the soil fungal or bacterial community composition or their extracellular enzyme activities. However, ericoid plant removal decreased microbial C:N ratio, suggesting a stoichiometric effect decoupled from microbial community composition. In other words, microbial communities appear to show initial plasticity in response to major changes in tundra vegetation. This highlights the importance of longer-term perspectives when investigating the effects of vegetation changes on biogeochemical processes in Arctic ecosystems.