Climate change impacts the characteristics of the vegetation carbon-uptake process in the northern Eurasian terrestrial ecosystem. However, the currently available direct CO2 flux measurement datasets, particularly for central Siberia, are insufficient for understanding the current condition in the northern Eurasian carbon cycle. Here, we report daily and seasonal interannual variations in CO2 fluxes and associated abiotic factors measured using eddy covariance in a coniferous forest and a bog near Zotino, Krasnoyarsk Krai, Russia, for April to early June, 2013–2017. Despite the snow not being completely melted, both ecosystems became weak net CO2 sinks if the air temperature was warm enough for photosynthesis. The forest became a net CO2 sink 7–16 days earlier than the bog. After the surface soil temperature exceeded ~1 °C, the ecosystems became persistent net CO2 sinks. Net ecosystem productivity was highest in 2015 for both ecosystems because of the anomalously high air temperature in May compared with other years. Our findings demonstrate that long-term monitoring of flux measurements at the site level, particularly during winter and its transition to spring, is essential for understanding the responses of the northern Eurasian ecosystem to spring warming.