Rising atmospheric concentrations of CO₂ and O₃ are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO₂ and O₃ (eCO₂ and eO₃) the endosphere, rhizosphere and soil were sampled from soybeans under eCO₂ and maize under eO₃. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO₂, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO₃ treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO₂ and O₃.