Windthrow-driven changes in carbon (C) allocation and soil microclimate can affect soil carbon dioxide (CO<sub>2</sub>) efflux (<i>F</i><sub>soil</sub>) from forest ecosystems. Although <i>F</i><sub>soil</sub> is the dominant C flux following stand-replacing disturbance, the effects of catastrophic windthrow on <i>F</i><sub>soil</sub> are still poorly understood. We measured <i>F</i><sub>soil</sub> at a montane mixed-forest site and at a subalpine spruce forest site from 2009 until 2012. Each site consisted of an undisturbed forest stand and two adjacent partially cleared (stem-fraction-harvested) windthrow areas, which differed with regard to the time since disturbance. The combination of chronosequence and direct time-series approaches enabled us to investigate <i>F</i><sub>soil</sub> dynamics over 12 years post-disturbance. At both sites <i>F</i><sub>soil</sub> rates did not differ significantly from those of the undisturbed stands in the initial phase after disturbance (1–6 years). In the later phase after disturbance (9–12 years), <i>F</i><sub>soil</sub> rates were significantly higher than in the corresponding undisturbed stand. 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 (15–31%) of <i>F</i><sub>soil</sub> from the windthrow areas was attributed to the increase in soil temperature. According to our estimates, ~500–700 g C m<sup>−2</sup> year<sup>−1</sup> are released via <i>F</i><sub>soil</sub> from south-facing forest sites in the Austrian Calcareous Alps in the initial 6 years after windthrow. With a high browsing pressure suppressing tree regeneration, post-disturbance net loss of ecosystem C to the atmosphere is likely to be substantial unless forest management is proactive in regenerating such sites. An increase in the frequency of forest disturbance by windthrow could therefore decrease soil C stocks and feed back positively on rising atmospheric CO<sub>2</sub> concentrations.