This study utilizes state-of-the-art in-situ measurements and advanced three-dimensional simulations to investigate the operation of a microwave plasma reactor for nitrogen fixation at a high subatmospheric pressure under various power inputs. It is shown that the system should be treated as a warm plasma due to negligible differences in vibrational and rotational temperatures and that it is required to account for chemical non-equilibrium. Complex flow field and significant temperature and concentration gradients are observed, emphasizing the need for three-dimensional simulations to accurately describe the interactions between mass, heat, and momentum transport and chemical reactions in non-equilibrium conditions. The innermost plasma regions reach temperatures close to 6000 K, while wall temperatures remain low due to presence of a low-temperature swirling flow field around the hot core. Analysis reveals that the swirling flow field around the hot core provides intrinsic partial quenching in regions with large temperature gradients which counteract the return to chemical equilibrium and enrich the flow surrounding the hot core. The inner flow exhibits a recirculation zone, stagnation point, and a transition into an increasingly parabolic flow profile closer to the reactor outlet. The agreement between the numerical modeling and the measurements is strong. In-situ Raman spectroscopy measurements confirm the calculated temperature field inside the reactor. Thermocouple measurements on the reactor wall are also in good agreement with the simulation. Additionally, Fourier-transform infrared spectroscopy measurements agree very well with the simulated amount of nitrogen oxide exiting the reactor at different microwave power inputs. The understanding and modeling capabilities are expected to support the development of future reactor designs that can facilitate higher yields.