The metal–semiconductor (M-S) junction based devices are commonly used in all sorts of electronic devices. Their electrical properties are defined by the metallic phase properties with a respect to the semiconductor used. Here we make an in-depth survey on the origin of the M-S junction at the atomic scale by studying the properties of the AuIn2 nanoelectrodes formed on the InP(0 0 1) surface by the in situ electrical measurements in combination with a detailed investigation of atomically resolved structure supported by the first-principle calculations of its local electrical properties. We have found that a different crystallographic orientation of the same metallic phase with a respect to the semiconductor structure influences strongly the M-S junction rectifying properties by subtle change of the metal Fermi level and influencing the band edge moving at the interface. This ultimately changes conductivity regime between Ohmic and Schottky type. The effect of crystallographic orientation has to be taken into account in the engineering of the M-S junction-based electronic devices.