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Summary: Here, we present a finite element method-based scheme for solving coupled partial differential equations (PDEs) for the analysis of lithiation-induced stress in largely deformed spherical nanoparticles via the PDE module in COMSOL. We describe steps for software installation and setting PDEs, initial/boundary conditions, and mesh parameters. We then detail procedures for dividing the mesh and analyzing lithium trapping during electrochemical cycling. This protocol can also be extended to analyze a wide range of problems involving diffusion-induced stress.For complete details on the use and execution of this protocol, please refer to Li et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.