Recent advancements in nuclear energy, particularly in the development of Molten Salt Reactors (MSRs), emphasize a shift towards integrating advanced technology for enhanced safety and efficiency. MSRs utilize unique fuel cycles and offer significant advantages over traditional reactors, including flexibility in fuel utilization and improved safety mechanisms. This study introduces a multiphysics species tracking framework developed within the Multiphysics Object-Oriented Simulation Environment (MOOSE), designed to model the intricate behaviors of species within MSR systems. The framework integrates neutron transport, thermal-hydraulics, and thermochemical dynamics, allowing for the analysis of species transport phenomena, including leaching, plating, and corrosion. The framework was applied to a generic Molten Salt Fast Reactor (MSFR) model, revealing critical insights into temperature-driven material leaching and plating processes. It demonstrated how temperature gradients and redox potential changes significantly influence the behavior of corrosion products, with specific concentrations tracked over time. Notably, the introduction of beryllium as a redox control measure was shown to mitigate corrosion by reducing the redox potential of the fuel salt. The findings underscore the importance of species tracking in MSRs for reactor safety, design optimization, and regulatory compliance. This research not only elucidates the dynamic interactions between various species in molten salt systems but also highlights the framework’s potential to guide future developments in MSR technology. The results indicate a clear pathway for enhancing reactor design and operational safety through informed modeling, paving the way for advanced nuclear reactor deployment in the near future. Future work will focus on validation against experimental data and further refinement of the framework to support ongoing advancements in MSR technology.