Fabry-Pérot (FP) etalons are used as filters and sensors in a range of optical systems. Often FP etalons are illuminated by collimated laser beams, in which case the transmitted and reflected light fields can be calculated analytically using well established models. However, FP etalons are sometimes illuminated by more complex beams such as focussed Gaussian beams, which may also be aberrated. Modelling the response of FP etalons to these beams requires a more sophisticated model. To address this need, we present a model that can describe the response of an FP etalon that is illuminated by an arbitrary beam. The model uses an electromagnetic wave description of light and can therefore compute the amplitude, phase and polarization of the optical field at any position in the system. It can also account for common light delivery and detection components such as lenses, optical fibres and photo-detectors, allowing practical systems to be simulated. The model was validated against wavelength resolved measurements of transmittance and reflectance obtained using a system consisting of an FP etalon illuminated by a focussed Gaussian beam. Experiments with focal spot sizes ranging from 30 µm to 250 µm and FP etalon mirror reflectivities in the range 97.2 % to 99.2 % yielded excellent visual agreement between simulated and experimental data and an average error below 10% for a range of quantitative comparative metrics. We expect the model to be a useful tool for designing, understanding and optimising systems that use FP etalons.