We have fabricated oxide based spin filter junctions in which we demonstrate that magnetic anisotropy can be used to tune the transport behavior of spin filter junctions. Until recently, spin filters have been largely comprised of polycrystalline materials where the spin filter barrier layer and one of the electrodes are ferromagnetic. These spin filter junctions have relied on the weak magnetic coupling between one ferromagnetic electrode and a barrier layer or the insertion of a nonmagnetic insulating layer in between the spin filter barrier and electrode. We have demonstrated spin filtering behavior in La0.7Sr0.3MnO3/chromite/Fe3O4 junctions without nonmagnetic spacer layers where the interface anisotropy plays a significant role in determining transport behavior. Detailed studies of chemical and magnetic structure at the interfaces indicate that abrupt changes in magnetic anisotropy across the non-isostructural interface is the cause of the significant suppression of junction magnetoresistance in junctions with MnCr2O4 barrier layers.