Elevated atmospheric CO₂ was often shown to stimulate belowground C allocation, but it is uncertain if this increase also alters the structure of soil microbial communities. Here, we assessed the effects of nine years of CO₂ enrichment on soil microbial communities of an alpine treeline ecosystem with 35-year-old Larix decidua and Pinus mugo ssp. uncinata trees. We also tracked the ¹³C signal of supplemental CO₂ in soil-respired CO₂, microbial biomass, and phospholipid fatty acids (PLFA) in undisturbed mor-type organic layers. We found a persistently increased soil CO₂ efflux (+24% on average), but negligible effects of elevated CO₂ on the biomass and community structure of soil microorganisms under both tree species determined with PLFA and T-RFLP (terminal restriction fragment length polymorphism). The ¹³C tracing over 9 years revealed that 24-40% of the soil microbial biomass was composed of ‘new’ plant-derived C. PLFA from gram-negative biomarkers did not significant shift in ¹³C by the CO₂ addition, while those of gram-negative bacteria were significantly altered. The highest ¹³C signals in individual PLFA was found in the fatty acid 18:2ω6,9 with 65-80% new C, indicating that new plant-derived C was primarily incorporated by soil fungi. However, CO₂ enrichment did not affect the production of mycelia biomass and the structure and composition of the fungal communities analysed by high-throughput 454-sequencing of genetic markers. Collectively, our results suggest that C flux through the plant-soil system will be accelerated but that the biomass and composition of microbial communities will be little affected by rising atmospheric CO₂ in organic matter rich treeline soils.