There is abundant evidence that greenhouse gas (GHG) emissions of cereal products, expressed per ton of grain output, have been trending downward over the past 20 years. This has largely been achieved through agricultural intensification that has concurrently increased area-based GHG emissions. The challenge is for agriculture to increase grain yields to meet the food demands of a growing world population while also contributing to climate stabilization goals by reducing net GHG emissions. This study assessed yield-based and area-based emissions and efficiencies for the winter wheat–summer maize (WWSM) rotation system over the period 1996 to 2016 using long-term, longitudinal, farm survey data and detailed soil emission data in Huantai county, Shandong Province, which is an archetype for cereal production across the North China Plain (NCP). In this region, yields have been increasing over time. However, nitrogen fertilizer inputs have decreased substantially with greater adoption of soil nutrient testing. In addition, there has been widespread adoption of residue incorporation into soils. As such, since 2002, the product carbon footprints of wheat and maize have reduced by 25% and 30%, respectively. Meanwhile, area-based carbon footprints for the rotation system have reduced by around 15% over the same period. These findings demonstrate the importance of detailed assessment of soil N2O emissions and rates of soil organic carbon sequestration. They also show the potential for net reductions in GHG emissions in cropping without loss of grain yields.