Climate change might alter annual snowfall patterns and modify the duration and magnitude of snow cover in temperate regions with resultant impacts on soil microclimate and soil CO2 efflux (Fsoil). We used a 5-year time series of Fsoil measurements from a mid-elevation forest to assess the effects of naturally changing snow cover. Snow cover varied considerably in duration (105–154 days) and depth (mean snow depth 19–59 cm). Periodically shallow snow cover (<10 cm) caused soil freezing or increased variation in soil temperature. This was mostly not reflected in Fsoil which tended to decrease gradually throughout winter. Progressively decreasing C substrate availability (identified by substrate induced respiration) likely over-rid the effects of slowly changing soil temperatures and determined the overall course of Fsoil. Cumulative CO2 efflux from beneath snow cover varied between 0.46 and 0.95 t C ha−1 yr−1 and amounted to between 6 and 12% of the annual efflux. When compared over a fixed interval (the longest period of snow cover during the 5 years), the cumulative CO2 efflux ranged between 0.77 and 1.18 t C ha−1 or between 11 and 15% of the annual soil CO2 efflux. The relative contribution (15%) was highest during the year with the shortest winter. Variations in snow cover were not reflected in the annual CO2 efflux (7.44–8.41 t C ha−1) which did not differ significantly between years and did not correlate with any snow parameter. Regional climate at our site was characterized by relatively high amounts of precipitation. Therefore, snow did not play a role in terms of water supply during the warm season and primarily affected cold season processes. The role of changing snow cover therefore seems rather marginal when compared to potential climate change effects on Fsoil during the warm season.