ABSTRACT The atmospheres of brown dwarfs have been long observed to exhibit a multitude of non-equilibrium chemical signatures and spectral variability across the L, T, and Y spectral types. We aim to investigate the link between the large-scale 3D atmospheric dynamics and time-dependent chemistry in the brown dwarf regime, and to assess its impact on spectral variability. We couple the miniature kinetic chemistry module ‘mini-chem’ to the Exo-FMS general circulation model (GCM). We then perform a series of idealized brown dwarf regime atmospheric models to investigate the dynamical 3D chemical structures produced by our simulations. The GCM output is post-processed using a 3D radiative transfer model to investigate hemisphere-dependent spectral signatures and rotational variability. Our results show the expected strong non-equilibrium chemical behaviour brought on by vertical mixing and global spatial variations due to zonal flows. Chemical species are generally globally homogenized, showing variations of ±10 per cent or less, dependent on pressure level, and follow the dynamical structures present in the atmosphere. However, we find localized storm regions and eddies can show higher contrasts, up to ±100 per cent, in mixing ratio compared to the background global mean. This initial study represents another step in understanding the connection between 3D atmospheric flows in brown dwarfs and their rich chemical inventories.