Excess CO<inf>2</inf> accumulated in soils is typically transported to the atmosphere through molecular diffusion along a concentration gradient. Because of the slow and constant nature of this process, a steady state between peat CO<inf>2</inf> production and emissions is often established. However, in peatland ecosystems, high peat porosity could foster additional non-diffusive transport processes, whose dynamics may become important to peat CO<inf>2</inf> storage, transport and emission. Based on a continuous record of in situ peat pore CO<inf>2</inf> concentration within the unsaturated zone of a raised bog in southern Canada, we show that changes in wind speed create large diel fluctuations in peat pore CO<inf>2</inf> store. Peat CO<inf>2</inf> builds up overnight and is regularly flushed out the following morning. Persistently high wind speed during the day maintains the peat CO<inf>2</inf> with concentrations close to that of the ambient air. At night, wind speed decreases and CO<inf>2</inf> production overtakes the transport rate leading to the accumulation of CO<inf>2</inf> in the peat. Our results indicate that the effective diffusion coefficient fluctuates based on wind speed and generally exceeds the estimated molecular diffusion coefficient. The balance between peat CO<inf>2</inf> accumulation and transport is most dynamic within the range of 0–2 m s⁻¹ wind speeds, which occurs over 75% of the growing season and dominates night-time measurements. Wind therefore drives considerable temporal dynamics in peat CO<inf>2</inf> transport and storage, particularly over sub-daily timescales, such that peat CO<inf>2</inf> emissions can only be directly related to biological production over longer timescales.