When spin current is transmitted across metal-molecule interfaces it is very sensitive to the fine details of the interfacial electronic structure. We use this sensitivity to demonstrate significant enhancement of anisotropic magnetoresistance in molecular junctions. The important role of the metal-molecule orientation is exemplified and used for fine tuning of anisotropic magnetoresistance by mechanical means. The presented effect is based on local formation of half metallicity using interface properties (D. Rakhmilevitch et al. Nano Letters 16, 1741 (2016)).