A recurring motif in soft matter and biophysics is modeling the mechanics of interacting particles on fluid membranes. One of the main outstanding challenges in these applications is the need to model the strong coupling between the substrate deformation and the particles’ positions as the latter freely move on the former. This work presents a thin-shell finite element formulation based on subdivision surfaces to compute equilibrium configurations of a thin fluid shell with embedded particles. We use a variational Lagrangian framework to couple the mechanics of the particles and the substrate without having to resort to ad hoc constraints to anchor the particles to the surface. Unlike established methods for such systems, the particles are allowed to move between elements of the finite element mesh. This is achieved by parametrizing the particle locations on the reference configuration. Using the Helfrich–Canham energy as a model for fluid shells, we present the finite element method’s implementation and an efficient search algorithm required to locate particles on the reference mesh. Several analyses with varying numbers of particles are finally presented reproducing symmetries observed in the classic Thomson problem and showcasing the coupling between interacting particles and deformable membranes.