Crop yields directly affect carbon (C) inputs into soils. Tillage management can influence crop performance, and as such should be considered when quantifying soil organic carbon (SOC) change, and thus net greenhouse gas emissions from croplands for national greenhouse gas inventory reporting. We conducted a meta-analysis of the effects of no-tillage (NT) and conventional tillage (CT) on crop yields for multiple crop species, soil types, and climatic regions of Canada. Yield response to NT varied between western and eastern Canada. Regardless of crop type, experiment duration, soil texture, and residue management, experiments in eastern Canada showed an average of 6% lower yields (p ≤ 0.005) under NT compared to CT. In western Canada, crop type had an important effect on yields between NT and CT with wheat, canola, and legumes exhibiting 10% (p ≤ 0.001), 7% (p ≤ 0.05), and 9% (p ≤ 0.05) higher yields on average under NT compared to CT, respectively. In western Canada, higher yields would be reflected in a similar scale of higher C inputs to NT systems. A recent meta-analysis of the effects of tillage management on SOC in Canada showed an 8% higher storage of SOC under NT systems compared to CT, a difference limited to western Canadian soils. Incorporating the effect of tillage on C inputs will lead to improvements in the accuracy of the effects of tillage management on SOC change in Canadian cropland. The activity data can be improved by applying weightings to the yield data by site-specific assessment of tillage practices across Canada.