The goal of this study is to experimentally validate PIXE modelling using the Geant4-ANSTO model (“G4-ANSTO”), distributed for the first time in Geant4 11.0, as well as the Geant4 default model (“G4-default”), for targets bombarded with carbon ions of energies up to 3 MeV/amu, an energy range of importance for PIXE applications. The experimental validation was performed using a variety of target materials, spanning a broad atomic number range. The reference experimental measurements were performed at the ANSTO heavy ion microprobe beamline ANTARES. To the authors’ knowledge, this is the first benchmarking investigation for PIXE simulations in Geant4 utilising carbon ions and it is significant for PIXE-based elemental analysis, encompassing archaeological samples, gas samples, environmental and planetary samples for geological and planetary research studies. It is also of relevance for any physics application, requiring the modelling of particle induced atomic de-excitation or atomic de-excitation only.