Abstract Amidst the global trend towards decarbonization, ammonia-diesel dual-fuel engines, which utilize ammonia port fuel injection and diesel direct injection to ignite ammonia-air premixed combustion, emerge as a viable option for heavy-duty applications. However, the characteristics of nitrogen-based pollutants in such engines are not well understood, largely due to the introduction of nitrogen-based fuels that enhance nitrogen reactivity during combustion. Since nitrogen-based pollutant emission features are governed by the fuel-borne nitrogen mechanism, this study investigates fuel-borne nitrogen pollutants in ammonia-diesel dual-fuel engines by rendering atmospheric nitrogen unreactive in the chemical mechanism of a three-dimensional (3D) computational fluid dynamics (CFD) model. Simulation results indicate that unburned ammonia is the primary nitrogen-based pollutant, with ammonia slip resulting from larger regions unreachable by the diesel diffusion flame and higher concentrations of ammonia in these areas. Additionally, concentrations of nitrous oxide (N2O) are found to be comparable to those of nitrogen oxides (NOx), primarily because the formed NOx is reduced by amino groups, while N2O continues to be produced during the late oxidation stage. Consequently, ammonia-diesel dual-fuel operation yields lower NOx concentrations compared to pure diesel operation, and an increased ammonia energy ratio further reduces NOx emissions. Among NOx species, nitric oxide (NO) concentrations remain predominant; however, nitrogen dioxide (NO2) plays a crucial role in the diesel auto-ignition process. The concentration of NO2 in the exhaust gases exhibits limited sensitivity to changes in the ammonia energy ratio. Despite these findings being derived from CFD simulations that deactivate nitrogen kinetics in the air, they help in understanding the nitrogen-based emission features of ammonia-diesel dual-fuel engines. Moreover, these findings underscore the complexity of nitrogen-based pollutant emissions in ammonia-diesel dual-fuel engines compared to traditional petroleum-fueled engines, highlighting the need for further fundamental research to develop effective control strategies for nitrogen-based pollutants and facilitate the market introduction of ammonia-diesel dual-fuel engines.