Overcoming the difficulty in reproducibility and deterministically defining the metal phase of metal-semiconductor heterojunctions is among the key prerequisites to enable next-generation nanoelectronic, optoelectronic and quantum devices. In this respect, a comprehensive understanding of the charge carrier injection and the electronic conduction mechanisms, which are distinctly different from conventional MOSFETs, are necessary. Here, we provide an in-depth discussion of the transport mechanisms in Si and Ge nanowires (NWs) embedded in Schottky barrier (SB) FETs (SBFETs). Key for the fabrication of these devices is the selective and controllable transformation of Si and Ge NWs into Al, which enables high-quality monolithic and single-crystalline Al contacts, fulfilling compatibility with modern CMOS fabrication. To investigate the transport in Al-Si and Al-Ge heterostructures, detailed and systematic electrical characterizations carried out by bias spectroscopy in the temperature regime between T = 77.5 K and 400 K. Thereof, activation energy maps have been extracted to evaluate the effective SB height for electrons and holes in both material systems. The Al-Si material system revealed symmetric effective SBs, which is interesting for reconfigurable electronics relying on reproducible nanojunctions with equal injection capabilities for electrons and holes. In stark contrast, the Al-Ge material system revealed a highly transparent contact for holes due to Fermi level pinning close the valance band and charge carrier injection saturation by a thinned SB, while thermionic and field emission mechanism limit the overall electron conduction. In this regime, nanometer scale Ge departs from its bulk counterpart and delivers a strong and reproducible negative differential resistance followed by a sudden current increase indicating the onset of impact ionization above a certain threshold electric field. Most importantly, the presented description of the temperature dependent transport mechanisms in Al-Si and Al-Ge nanojunctions contributes to a better understanding of metal-group-IV based SBFETs, which are highly anticipated for the implementation of electronic device functionalities beyond the capabilities of conventional FETs.