CONTEXTFarming systems face dual pressures of reducing greenhouse gas (GHG) emissions to mitigate climate change and safeguarding food security to adapt to climate change. Building soil organic carbon (SOC) is proposed as a key strategy for climate change mitigation and adaptation. However, practices that increase SOC may also increase nitrous oxide (N2O) emissions, and impact crop yields and on-farm income. A comprehensive assessment of the effects of different management practices on trade-offs between GHG emissions and agricultural systems profitability under climate change is needed. OBJECTIVEWe aimed to: (1) analyze the long-term trends of SOC and N2O emissions, and ascertain whether the croplands of the study region are net GHG sources or sinks under climate change; (2) quantify the GHG abatement on a gross margin basis; (3) identify effective management practices that could achieve a win-win strategy; and (4) investigate sources of uncertainty in estimates of GHG emissions and gross margins under climate change. METHODSAPSIM was used to simulate the effects of three crop residue retention rates (10%, 50% and 100%), and six representative crop rotations (wheat-canola, wheat-field pea-wheat-canola, wheat-field pea-wheat-oats, wheat-wheat-barley, wheat-wheat-canola, and wheat-wheat-oats) under two Shared Socio-economic Pathways scenarios (SSP245 and SSP585) using climate projections from 27 GCMs. GHG emissions and gross margins from 1961 to 2092 were assessed across 204 study sites in southeastern Australia. RESULTS AND CONCLUSIONSOur results showed that residue retention can turn the soil from a carbon source (10% retention, 304–450 kg CO2-eq ha−1 yr−1) to a carbon sink (100% retention, −269 ∼ −57 kg CO2-eq ha−1 yr−1), and the potential of carbon sequestration was partly offset by concomitantly increased N2O emissions. The wheat-wheat-canola rotation with full residue retention was shown to be a win-win solution with both large potential of GHG abatement and high gross margin compared with other rotations. Spatial analysis showed that the southeastern part of the study region, with higher rainfall, had higher gross margins, while the drier northwestern part had greater GHG emission reduction potentials. Although climate change led to increased GHG emissions and decreased yields for some crops, these adverse effects were overweighed by the higher SOC and yield advantages from full residue retention. SIGNIFICANCEThis study emphasizes the significant potential for agronomic management to maximize gross margin and reduce GHG emissions under climate change in southeast Australia. Results from this study could be used by farmers and policymakers to mitigate climate change without compromising agroecosystem profitability.