Crop rotations are considered a promising strategy for mitigating greenhouse gas (GHG) emissions and enhancing soil organic matter in agricultural land. However, studies often focused solely on either GHG emissions or soil organic carbon (SOC) changes, rather than integrating both indicators. We conducted a 4-year (2018-2021) crop rotation study to examine effects of six rotation systems in three ecoregions (sub-humid, sub-semiarid, and semiarid) on GHG emissions, SOC changes, and C footprints in Saskatchewan, Canada. The six rotation systems include (i) control, (ii) intensified, (iii) diversified, (iv) market-driven, (v) high-risk, and (vi) soil-health cropping system. GHG emissions were estimated using the Holos model, and SOC changes were estimated using the Campbell model, and C footprints were calculated as the difference between GHG emissions and SOC changes. The 4-year cumulative GHG emissions, expressed as CO2 equivalent (CO(2)e), were highest in the sub-humid ecoregion due to higher background SOC levels, nitrogen (N) fertilizer inputs, and precipitation. The diversified and soil-health systems reduced GHG emissions by reduced N fertilizer inputs. Carbon footprints revealed net CO(2)e emissions for the market-driven system but net CO(2)e withdrawals for the soil-health and diversified systems. The results indicated that the diversified systems significantly mitigated GHG emissions, increased soil C stocks, and withdrew CO(2)e.