Abstract The very high energy (VHE) emission of the central molecular zone (CMZ) is rarely modeled in 3D. Most approaches describe the morphology in 1D or simplify the diffusion to the isotropic case. In this work, we show the impact of a realistic 3D magnetic field configuration and gas distribution on the VHE γ-ray distribution of the CMZ. We solve the 3D cosmic-ray transport equation with an anisotropic diffusion tensor using the approach of stochastic differential equations as implemented in the CRPropa framework. We test two different source distributions for five different anisotropies of the diffusion tensor, covering the range of effectively fieldline-parallel diffusion to isotropic diffusion. Within the tested magnetic field configuration, the anisotropy of the diffusion tensor is close to the isotropic case, and three point sources within the CMZ are favored. Future missions such as the upcoming CTA will reveal more small-scale structures that are not yet included in the model. Therefore, a more detailed 3D gas distribution and magnetic field structure will be needed.