Hemiboreal forests form a transitional belt between boreal and temperate forests in Eurasia, and due to long-term climate warming they could potentially expand in a northerly direction. However, carbon (C) exchange studies in this transitional forest type are scarce. In 2014–2015 we analyzed CO2 exchange in a hemiboreal mixed forest at SMEAR Estonia (Station for Measuring Ecosystem-Atmosphere Relations) using eddy covariance (EC), soil chamber technique and biometric methods. Employing two plots that differ in forest stand composition (mixed (MP) and coniferous (CP)) located within the footprint of the EC tower, we evaluated heterotrophic and total soil respiration (Rh and Rs, respectively). Measurements showed that C, nitrogen (N), and soil organic matter (SOM) contents in topsoil were significantly higher in the coniferous plot, and the total C stock until 20 cm of mineral soil was higher by a factor of two (i.e., 170.6 and 94.8 t C ha−1 for the CP and MP, respectively). Only in 2015 there was a significant difference in Rs between the plots, while Rh exhibited no detectable difference. The cumulative Rs during the growing season was similar for both plots (CP and MP) and years: 532 and 548 g m−2, respectively, in 2014; 636 and 592 g m−2, respectively, in 2015. The same applied to Rh: 418 and 430 g m−2, respectively, in 2014; 406 and 387 g m−2, respectively, in 2015.The forest as a whole was a C sink. In 2015, net ecosystem exchange (NEE) was -585.62 ± 45.16 g C m−2 yr−1 (the average and SD of two gap-filling methods: MDS and nonlinear regressions). Gross primary production (GPP), and ecosystem respiration (RE) were -1280.62 ± 53.36, and 696.00 ± 98.51 g C m−2 yr−1, respectively (the average and SD of two flux partitioning methods: nighttime data-based and daytime data-based). NEE and GPP suggested a greater similarity to temperate forests, while RE was closer to more boreal forest stands.The mean value of net ecosystem production (NEP) of both plots, estimated using forest stand biometric, litter and chamber data was similar to the annual NEE value: 6.3 and −5.9 t C ha−1 yr−1, respectively.