Metal-Semiconductor (M/S) heterojunctions, better known as Schottky junctions play a crucial role in modern electronics. At present, the mechanisms behind the M/S junctions are still a subject of discussion. In this work, we investigate the interfaces between semiconducting crystalline Si and amorphous metallic indium, Si{0 0 1}/a-In and Si{1 1 1}/a-In using both ab initio molecular dynamics simulations and a Schottky-Mott approach. The simulations reveal the formation of a distinct border between the Si substrates and amorphous In at the interfaces. The In atoms adjacent to the interfaces exhibit atomic ordering. Charge transfer occurs from In to Si, forming c-Si-q/a-In+q charge barriers at the interfaces. This indicates that a crystalline p-Si/a-In heterojunction will have rectifying properties, which agrees with an analysis using the Schottky-Mott model which predicts a Schottky barrier height of 1.3 eV for crystalline p-Si/a-In using the calculated work function for a-In (3.82 eV). We further discuss the interfacial charge transfer, related hole-depletion regions in Si adjacent to the interfaces and the Schottky-Mott approximations.