The association between the responses of microbial activity and residue decomposition to elevated atmospheric [CO2] under field conditions in Australian cropping systems is unknown. We measured soil CO2 emission and decomposition of wheat and field pea residues in a wheat cropping system in the field using the Australian Grains Free-Air CO2 Enrichment (AGFACE) facility in Horsham, Victoria. Elevated [CO2] (550 μmol mol−1) increased soil CO2 emission by 41%, but did not affect the percentage of the original mass or C remaining for either type of residue throughout the experimental period. Our findings suggest that the rates of residue decomposition and residue C mineralization in this semi-arid wheat cropping system were not affected by elevated [CO2] despite higher microbial activity. This has major implication for the C sequestration potential of semi-arid cropping systems under future CO2 climates.