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This paper presents a novel approach employing localized annealing through Joule heating to enhance the performance of Thin-Film Piezoelectric-on-Silicon (TPoS) MEMS resonators that are crucial for applications in sensing, energy harvesting, frequency filtering, and timing control. Despite recent advancements, piezoelectric MEMS resonators still suffer from anchor-related energy losses and limited quality factors (Qs), posing significant challenges for high-performance applications. This study investigates interface modification to boost the quality factor (Q) and reduce the motional resistance, thus improving the electromechanical coupling coefficient and reducing insertion loss. To balance the trade-off between device miniaturization and performance, this work uniquely applies DC current-induced localized annealing to TPoS MEMS resonators, facilitating metal diffusion at the interface. This process results in the formation of platinum silicide, modifying the resonator’s stiffness and density, consequently enhancing the acoustic velocity and mitigating the side-supporting anchor-related energy dissipations. Experimental results demonstrate a Q-factor enhancement of over 300% (from 916 to 3632) and a reduction in insertion loss by more than 14 dB, underscoring the efficacy of this method for reducing anchor-related dissipations due to the highest annealing temperature at the anchors. The findings not only confirm the feasibility of Joule heating for interface modifications in MEMS resonators but also set a foundation for advancements of this post-fabrication thermal treatment technology.