Platinum-based thin films are widely used to create microelectronic devices operating at temperatures above 500 °C. One of the most effective ways to increase the high-temperature stability of platinum-based films involves incorporating refractory metal oxides (e.g., ZrO₂, HfO₂). In such structures, refractory oxide is located along the metal grain boundaries and hinders the mobility of Pt atoms. However, the effect of annealing conditions on the morphology and functional properties of such multiphase systems is rarely studied. Here, we show that the two-step annealing of 250-nm-thick Pt-Rh/Zr multilayer films instead of the widely used isothermal annealing leads to a more uniform film morphology without voids and hillocks. The composition and morphology of as-deposited and annealed films were investigated using X-ray diffraction and scanning electron microscopy, combined with energy-dispersive X-ray spectroscopy. At the first annealing step at 450 °C, zirconium oxidation was observed. The second high-temperature annealing at 800–1000 °C resulted in the recrystallization of the Pt-Rh alloy. In comparison to the one-step annealing of Pt-Rh and Pt-Rh/Zr films, after two-step annealing, the metal phase in the Pt-Rh/Zr films has a smaller grain size and a less pronounced texture in the direction, manifesting enhanced high-temperature stability. After two-step annealing at 450/900 °C, the Pt-Rh/Zr thin film possessed a grain size of 60 ± 27 nm and a resistivity of 17 × 10⁻⁶ Ω·m. The proposed annealing protocol can be used to create thin-film MEMS devices for operation at elevated temperatures, e.g., microheater-based gas sensors.