Abstract We studied the evolution of an isolated pulsed plasma in a vortex flow stabilised microwave (MW) discharge in N₂ at 25 mbar via the combination of 0D kinetics modelling, iCCD imaging and laser scattering diagnostics. Quenching of electronically excited N₂ results in fast gas heating and the onset of a thermal-ionisation instability, contracting the discharge volume. The onset of a thermal-ionisation instability driven by vibrational excitation pathways is found to facilitate significantly higher N₂ conversion (i.e. dissociation to atomic N₂) compared to pre-instability conditions, emphasizing the potential utility of this dynamic in future fixation applications. The instability onset is found to be instigated by super-elastic heating of the electron energy distribution tail via vibrationally excited N₂. Radial contraction of the discharge to the skin depth is found to occur post instability, while the axial elongation is found to be temporarily contracted during the thermal instability onset. An increase in power reflection during the thermal instability onset eventually limits the destabilising effects of exothermic electronically excited N₂ quenching. Translational and vibrational temperature reach a quasi-non-equilibrium after the discharge contraction, with translational temperatures reaching ∼1200 K at the pulse end, while vibrational temperatures are found in near equilibrium with the electron energy (1 eV, or ∼11 600 K). This first description of the importance of electronically excited N₂ quenching in thermal instabilities gives an additional fundamental understanding of N₂ plasma behaviour in pulsed MW context, and thereby brings the eventual implementation of this novel N₂ fixation method one step closer.