Windthrow driven changes in carbon (C) allocation and soil microclimate can affect soil carbon dioxide (CO 2 ) efflux ( F soil ) of forest ecosystems. Although F soil is the dominant C flux following stand-replacing disturbance, the effects of catastrophic windthrow on F soil are still poorly understood. We measured F soil at a montane mixed forest site and at a subalpine spruce forest site from 2009 until 2012. Both sites consisted of undisturbed forest stands and two adjacent windthrow areas which differed in time since disturbance. The combination of chronosequence and direct time-series approaches enabled us to investigate F soil dynamics over 12 years post-disturbance. In the initial phase after disturbance (1–6 years), F soil rates did not differ significantly from those of the undisturbed stands, but in the later phase (9–12 years after disturbance) F soil rates were significantly higher than corresponding undisturbed stand values. The higher F soil rates in the later phase post-disturbance are likely explained by a dense vegetation cover and correspondingly higher autotrophic respiration rates. Soil temperature increased significantly following windthrow (by 2.9–4.8 °C) especially in the initial phase post-disturbance when vegetation cover was sparse. A significant part (20–36%) of F soil from the windthrow areas was thus attributed to disturbance induced changes in soil temperature. According to our estimates, ~500 to 700 g C m −2 yr −1 are released via F soil from south-facing forest sites in the Austrian Calcareous Alps in the initial 6 years after windthrow. With high game pressure suppressing primary production in these areas, post-disturbance loss of ecosystem C to the atmosphere is likely to be substantial unless management is proactive in regenerating such sites. An increase in the frequency of forest disturbance by windthrow could therefore decrease soil C stocks and positively feedback on rising atmospheric CO 2 concentrations.