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Expansion of cropland involves immense land use changes, and the resulting intensified management practices have a strong influence on the functioning of the underlying soil. For instance, increased application of nitrogen (N) fertilizer is known to enhance fluxes of nitrous oxide (N2O) from the soil to the atmosphere. The emission factor (EF) proposed by the Intergovernmental Panel on Climate Change (IPCC) assumes a linear relationship between added N and N2O-N fluxes, but it does not account for environmental factors, such as soil properties or climate. Due to the high spatial and temporal variability of N2O-N fluxes, mechanistic models are preferable in terms of extrapolation to larger scales. In this study, we evaluated simulated N2O-N fluxes from soils under agricultural use in the Brazilian state, Mato Grosso, using the CANDY (Carbon and Nitrogen Dynamics) model. A control tool was developed in order to enable the simulation of 1 650 scenarios covering different sites (soil + climate) and management regimes (crop rotation + amount of applied fertilizer + sowing and harvesting dates). Results suggested that the sites had a very strong influence on calculated emissions, which is not accounted for by static EF. Furthermore, most fertilizer-induced N2O-N fluxes derived from the scenario simulations were best described by a non-linear function. For sounder budgeting on the federal and national scale, there is still a strong need for long-term observations of continuous crop rotations and spatial distribution of soil types and their specific characteristics. The presented results provide a valuable starting point for developing further scenario simulations and adapting experimental campaigns for N2O emission study.