Annual horticultural systems rely on frequent and intensive tillage to prepare beds, manage weeds and control insects. But this practice reduces soil organic carbon (SOC) through accelerated CO2 emission. Crop residue incorporation could counteract this loss. We investigated whether vegetable systems could be made more resilient by including a high-residue grain crop such as sweet corn (Zea mays L. var. rugosa), in the rotation through the use of conventional (no residue, no soil sieving) and organic (residue incorporated and soil sieved) soil management scenarios. We evaluated short-term emission of CO2-C and soil C content in incubated Chromosol and Vertosol soils (Australian Classification) with and without sieving (simulated tillage) or the incorporation of ground sweet corn residue. Residue treatment emitted 2.3 times more CO2-C compared to the no-residue treatment, and furthermore, sieved soil emitted 1.5 times more CO2-C than the unsieved across the two soil types. The residue incorporation had a greater effect on CO2-C flux than simulated tillage, suggesting that C availability and form can be more important than physical disturbance in cropping soils. The organic scenario (with residue and sieved) emitted more CO2-C, but had 13% more SOC compared with the conventional scenario (without residue and unsieved), indicating that organic systems may retain more SOC than a conventional system. The SOC lost by soil disturbance was more than offset by the incorporation of residue in the laboratory conditions. Therefore, the possible SOC loss by tillage for weed control under organic management may be offset by organic residue input.