Research is ongoing to develop ways to reduce emissions of greenhouse gases (GHGs) from agricultural sources. A convenient technique to estimate emissions is to develop emission factors for a wide range of management practices. Default emission factors such as those given in the Intergovernmental Panel on Climate Change Tier I methodology are often used but these can result in substantial errors when applied to specific geographical regions. In this paper an interface was developed to link soil, climate and agricultural activity data in Canada with the DeNitrification and DeComposition (DNDC) model to create a modeling tool for estimating emission factors for changes in agricultural management. This tool was also designed to calculate country-specific IPCC Tier II emission factors for comparison against modeled results. The DNDC-Management Factor Tool (DNDC-MFT) was developed to automatically generate soil, climate and agricultural management model input data from national databases for estimating emissions factors for any of 462 ecodistricts across Canada. Six ecodistricts were selected across the major climatic regions to test the tool. The emission factors generated by the DNDC model were significantly different from Tier II values. Much variability in N2O emission estimates exist, partly due to limitations in certain biophysical processes in the model and partly due to quality of input data. The DNDC model is very sensitive to climate, size of initial soil C levels, and fertilizer application rates. We should also keep in mind that there is uncertainly associated with Tier II emission factors. The combined N2O and soil C factors estimated by the DNDC model are generally comparable to values that are being used to estimate Canada's national inventory (Tier II/III) but only the tillage factor was found to be statistically similar. The DNDC-MFT will be useful for testing the ability of the DNDC model to generate GHG emission factors for many management scenarios across varying climatic regions in Canada. The framework can be extended to include improved versions of DNDC and other ecosystem models.