Acceleration and storage of beams of relativistic partially stripped ions is more challenging than in the case of fully stripped ions because the interactions with matter, such as those with residual gas and collimators can strip electrons via ionisation. BDSIM is a code for the simulation of energy deposition and charged particle backgrounds in accelerators that uses the Geant4 physics library. Geant4 includes a broad range of ion elastic and inelastic interactions and allows the definition of partially stripped ion beams. However, no models are currently available to handle in-flight interactions involving the bound electrons. In this paper we present a semi-empirical model of beam ion stripping by material atoms that is implemented in BDSIM as an extension of Geant4’s existing physics processes and is fully integrated into a comprehensive set of matter interactions for partially stripped ions. The stripping cross-section for select cases and results from comprehensive simulations are presented.