Development of in-core instrumentation is driven by the pursuit of safer and more economic energy production from both existing nuclear reactors and Generation IV reactor designs. Idaho National Laboratory (INL) has developed high temperature irradiation resistant thermocouples (HTIR-TCs) for temperature sensing inside Generation IV nuclear reactors. These thermocouples are composed of phosphorus-doped niobium (Nb-P) and lanthana-doped molybdenum (Mo-LaO) thermoelements, an alumina (Al2O3) insulation, and a niobium sheath. HTIR-TCs require an initial heat treatment exceeding the maximum service temperature to stabilize the generated electromotive force (EMF) signal; however, the mechanism behind this stabilization is not well understood. This work evaluates the impact of Joule heating on the thermoelements’ microstructures, chemical stability, and mechanical properties to determine the mechanisms by which the EMF signal stabilization occurs. Accordingly, during the Joule heat treatment, a secondary Nb3P phase coarsened along the length of the Nb-P thermoelement, along with the formation of an interaction region at the Al2O3/niobium interface. The interaction between the alumina insulation and the Nb-P thermoelement was also observed within the Mo-LaO thermoelement. Joule heating induced stability within the generated EMF signal of HTIR-TCs through the formation of secondary phases within the Nb-P and the interaction of the alumina insulation with the thermoelements.