In the first half of 2020, Siberia experienced an intense and persistent heatwave (HW). This HW induced earlier and stronger CO2 uptake in the early growing season compared to previous years, which then led to reduced CO2 uptake in the late growing season partly due to soil desiccation, that is, seasonal legacy effects. Using the land surface model ORCHIDEE-MICT, we investigated whether the 2020 HW influenced the ecosystem processes in the following year 2021 (legacy effects) by the differences between simulation results with the observed climate forcing in 2020 and counterfactual simulations without a prominent HW event in 2020. The 2020 HW, combined with increased snowfall in late 2020, resulted in a 1.2°C warmer soil temperature, 20 kg m−2 more soil water content (in the top 1 m), and a 0.04 gC m−2 day−1 increase in heterotrophic respiration (CO2 emissions) in early 2021 in central Siberia. The 2020 HW also affected photosynthesis (CO2 uptake) in early summer 2021, with contrasting responses between biomes: CO2 uptake increased in forests (i.e., positive legacy effects), while it decreased in grasslands (i.e., small negative legacy effects). Due to the 2020 HW, forests gained 6 gC m−2 on land (combined plant and soil carbon), while grasslands lost 10.9 gC m−2. Our results highlight that the effects of HWs can persist aboveground (vegetation) and belowground (soil temperature and moisture) and significantly affect carbon pools and net CO2 fluxes in the following year.