Wintertime respiration contributes significantly to the annual loss of carbon from terrestrial ecosystems to the atmosphere, but the magnitude and physical transport mechanisms of this flux through snow remain unclear. Here, we quantify wintertime soil CO2 efflux in a Lodgepole pine (Pinus contorta Dougl.) forest by comparing chamber, flux gradient, and subcanopy eddy covariance measurements. CO2 efflux estimates from the flux gradient system deviated from the eddy covariance measurements during early and late winter but were only ca. 25% lower than eddy covariance measurements during the main snow accumulation period in mid-winter. During the snow-covered period, the flux gradient carbon efflux estimate (15 g C m− 2) was ca. three-fold less than eddy covariance measurements (49 g C m− 2). An analysis of the relationship between friction velocity and eddy covariance-measured CO2 efflux lends support to the notion that advection through snow is an important transport mechanism for trace gasses. A spectral Granger causality analysis indicates that the wind speed time series contributes information to the subnivean CO2 concentration time series during the melt period at time scales greater than 10 hours. All three methodologies indicate that wintertime respiration is a major contributor to the annual carbon budget: the sum of eddy covariance-measured CO2 efflux during the snow-covered period was 1/3 of that during the snow-free period of 2011 (ca. 140 g C m− 2). Future studies should incorporate adjustments for advection when using snow flux gradient systems to avoid underestimating the often-underappreciated contribution of the cold season to ecosystem CO2 efflux.