Topological systems, including for instance topological insulators, Dirac and Weyl semimetals, have attracted wide interest in the scientific community owing to their unconventional properties, such as giant thermoelectric and magnetoresistance effects, topological protection and quantum oscillations, which may be exploited for novel microelectronic and quantum applications. In the landscape of topological materials, CoSi has been recently identified as a nearly-ideal topological conductor which can potentially outperform conventional conducting materials.– To date, most of the investigations on topological CoSi focused on bulk single crystals, ; however, the relation between structural, electric and magnetotransport properties is still largely unexplored when the length scale of CoSi is decreased to the nanoscale. In this respect the investigation of CoSi thin films is of particular interest for the potential exploitation of its topological properties in novel microelectronic devices. In our work we have studied the correlation between microstructure and magnetotransport properties in CoSi thin films (thickness ≈ 20 nm) grown onto MgO substrates by molecular beam epitaxy. The evolution of the structural characteristics upon variation of the growth temperature from 30 to 450 ̊C reveals a systematic transition from amorphous to polycrystalline CoSi thin films. It is found that a higher degree of crystallinity brings about an augmented residual resistivity ratio and magnetoresistance. Nonetheless, the most striking influence of the modification of the CoSi microstructure is observed with respect to the analysis of the Hall effect. Amorphous CoSi films feature an anomalous Hall effect with electrons being the dominant charge carriers, whereas polycrystalline CoSi films undergo a transition towards a hole-dominated Hall transport regime. Our results unveil the complex interplay between structural and magnetotransport properties in CoSi thin films and pave the way towards their implementation in nanoscale devices.