Compared to fossil fuels, ammonia is an environmentally friendly, cost-effective, and readily available fuel that carries hydrogen. It is expected to play a crucial role in the development of carbon-neutral internal combustion engines for the next generation. However, a significant challenge arises due to the presence of nitrogen in both the fuel and air, leading to the complex generation of intertwined thermal and fuel-based nitrogen oxides (NOx) during ammonia combustion. To gain a deeper understanding of NOx emission characteristics and propose effective technologies for controlling NOx emissions from ammonia engines, it is essential to decouple the mechanisms responsible for thermal and fuel-based NOx and analyze the formation and evolution of both types separately. In this study, a novel approach employing argon circulation is applied to eliminate the thermal NOx formation mechanism. This allows for a detailed investigation of fuel-based NOx emissions in ammonia spark ignition engines. The results reveal that nitric oxide (NO) species still dominates, accounting for over 98% of the fuel NOx emissions under the investigated conditions. Furthermore, fuel NOx exhibits distinct concentration distribution patterns within the combustion chamber and displays a different relationship with engine control variables compared to thermal NOx. Specifically, fuel-based NOx is likely produced as a by-product of chemical equilibrium calculations within the flame front, with subsequent evolution within the burned zone. Moreover, fuel-based NOx increases with delayed spark timing, in contrast to the trend observed for thermal NOx. Lean operation favors fuel NOx formation, although excessively lean operation reduces NOx due to a lower nitrogen content in the fuel-oxidizer mixture. On the other hand, rich operation prevents NOx formation because of the ammonia’s de-NOx effect. The emissions of nitrous oxide (N2O) in the exhaust gases primarily originate from newly formed N2O during the late oxidation stage. Of these N2O, a portion of N2O is formed close to the cold walls, and another portion results from the partial oxidation of ammonia released from the crevice volume, where ammonia is trapped during the primary combustion stage. Lean operation promotes N2O formation and should be avoided to minimize its emissions. In conclusion, the implementation of the argon circulation system successfully elucidates the characteristics of fuel NOx formation in engines, which have been fully addressed in previous discussions. Moreover, this approach can also be extended to other engine types, such as ammonia-methane spark ignition engines, ammonia-hydrogen spark ignition engines, and compression ignition engines converted to ammonia-diesel dual-fuel engines.