Spatial diffusion under the influence of the Galactic magnetic field (GMF) plays a crucial role in the transport of cosmic-ray protons. The standard assumption is that the GMF is purely azimuthal and the diffusion process can be considered to be uniform and isotropic all across the Galaxy. However, this picture might be inaccurate, since both theoretical arguments and numerical simulations predict that diffusion might exhibit different features, depending on its being parallel or perpendicular to the direction of the magnetic field. This might have a large impact in the Galactic Center region, where the GMF presents a strong out-of-plane component. In particular, an anisotropic diffusion could contribute in determining the non-uniform density and energy distribution of cosmic-ray protons that is inferred from the measurements of the gamma-ray emissivity along the Galactic plane. In this talk we discuss how anisotropic cosmic-ray diffusion can be implemented within a realistic model of cosmic-rays transport. In particular, we investigate how the various features in the modelling of the GMF can impact the spatial and energetic distribution of cosmic-ray protons and we illustrate how this can be related to the most recent gamma-ray observations.