Cold gas and dust reprocess the central X-ray emission of active galactic nuclei (AGN), producing characteristic spectro-polarimetric features in the X-ray band. The recent launch of IXPE allows for observations of this X-ray polarisation signal, which encodes unique information on the parsec-scale circumnuclear medium of obscured AGN. However, the models for interpreting these polarimetric data are under-explored and do not reach the same level of sophistication as the corresponding spectral models. We aim at closing the gap between the spectral and spectro-polarimetric modelling of AGN circumnuclear media in the X-ray band by providing the tools for simulating X-ray polarisation in complex geometries of cold gas alongside X-ray spectra. We lay out the framework for X-ray polarisation in 3D radiative transfer simulations and provide an implementation to the 3D radiative transfer code SKIRT, focussing on (de)polarisation due to scattering and fluorescent re-emission. As an application, we explored the spectro-polarimetric properties of a 2D toroidal reprocessor of cold gas, modelling the circumnuclear medium of AGN. For the 2D torus model, we find a complex behaviour of the polarisation angle with photon energy, which we interpret as a balance between the reprocessed photon flux originating from different sky regions, with a direct link to the torus geometry. We calculated a large grid of AGN torus models and demonstrated how spatially resolved X-ray polarisation maps could form a useful tool for interpreting the geometrical information that is encoded in IXPE observations. With this work, we release high-resolution AGN torus templates that simultaneously describe X-ray spectra and spectro-polarimetry for observational data fitting with XSPEC. The SKIRT code can now model X-ray polarisation simultaneously with X-ray spectra and provide synthetic spectro-polarimetric observations for complex 3D circumnuclear media, with all features of the established SKIRT framework available.