The effects of heat and mass transfer on three-dimensional (3D) MHD free convective flow of a viscous incompressible fluid through a highly porosity medium with periodic permeability in the presence of chemical reaction have been studied. Presence of periodic permeability contributed to three-dimensional flow. In view of the periodic permeability, the solutions of the coupled non-linear equations of the main flow are assumed as the superimposition of a perturbed solutions with a small amplitude of variation on the two-dimensional (2D) flow with a small amplitude of variation which is quite justified. The effects of the pertinent parameters are shown with the help of graphs and tables. Interesting and expected results include the significant contribution of buoyancy effect in enhancing the velocity field whereas Lorentz force, endothermic reaction, periodic permeability reduce it. Rate of mass transfer on the surface decreases due to endothermic reaction with heavier diffusing species.