In the present open‐top chamber experiment, two silver birch clones (Betula pendula Roth, clone 4 and clone 80) were exposed to elevated levels of carbon dioxide (CO₂) and ozone (O₃), singly and in combination, and soil CO₂ efflux was measured 14 times during three consecutive growing seasons (1999–2001). In the beginning of the experiment, all experimental trees were 7 years old and during the experiment the trees were growing in sandy field soil and fertilized regularly. In general, elevated O₃ caused soil CO₂ efflux stimulation during most measurement days and this stimulation enhanced towards the end of the experiment. The overall soil respiration response to CO₂ was dependent on the genotype, as the soil CO₂ efflux below clone 80 trees was enhanced and below clone 4 trees was decreased under elevated CO₂ treatments. Like the O₃ impact, this clonal difference in soil respiration response to CO₂ increased as the experiment progressed. Although the O₃ impact did not differ significantly between clones, a significant time × clone × CO₂× O₃ interaction revealed that the O₃‐induced stimulation of soil respiration was counteracted by elevated CO₂ in clone 4 on most measurement days, whereas in clone 80, the effect of elevated CO₂ and O₃ in combination was almost constantly additive during the 3‐year experiment. Altogether, the root or above‐ground biomass results were only partly parallel with the observed soil CO₂ efflux responses. In conclusion, our data show that O₃ impacts may appear first in the below‐ground processes and that relatively long‐term O₃ exposure had a cumulative effect on soil CO₂ efflux. Although the soil respiration response to elevated CO₂ depended on the tree genotype as a result of which the O₃ stress response might vary considerably within a single tree species under elevated CO₂, the present experiment nonetheless indicates that O₃ stress is a significant factor affecting the carbon cycling in northern forest ecosystems.