Macroscopic current-voltage measurements and nanoscopic Ballistic Electron Emission Spectroscopy (BEES) have been used to probe the Schottky barrier height at metal/Ge(100) junctions for two metal electrodes (Au, Pt) and different metallization methods; specifically, thermal-vapour and laser-vapour deposition. Analysis of macroscopic current-voltage characteristics indicates that a Schottky barrier height of 0.61-0.63 eV controls rectification at room temperature. On the other hand, BEES measured at 80 K reveals the coexistence of two distinct barriers at the nanoscale, taking values in the ranges 0.61-0.64 eV and 0.70-0.74 eV for the cases studied. For each metal/semiconductor junction, the macroscopic measurement agrees well with the lower barrier found with BEES. Ab-initio modelling of BEES spectra ascribes the two barriers to two different atomic registries between the metals and the Ge(100) surface, a significant relevant insight for next-generation highly miniaturized Ge-based devices.