The concentrations of atmospheric carbon dioxide (CO 2 ) and tropospheric ozone (O 3 ) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO 2 (eCO 2 ) and elevated O 3 (eO 3 ) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO 2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO 2 , eO 3 or eCO 2 þ eO 3 . Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO 2 , whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO 3 , resulting in the fact that the abundance of some eO 3 -supressed genes was promoted to ambient, or eCO 2 -induced levels by the interaction of eCO 2 þ eO 3 . Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO 2 , the inhibition of N functional processes by eO 3 and the interaction by eCO 2 and eO 3 . This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems.