In recent times the chiral semimetal cobalt monosilicide (CoSi) has emerged as a prototypical, nearly ideal topological conductor hosting giant, topologically protected Fermi arcs. Exotic topological quantum properties have already been identified in CoSi bulk single crystals. However, CoSi is also known for being prone to intrinsic disorder and inhomogeneities, which, despite topological protection, risk jeopardizing its topological transport features. Alternatively, topology may be stabilized by disorder, suggesting the tantalizing possibility of an amorphous variant of a topological metal, yet to be discovered. In this respect, understanding how microstructure and stoichiometry affect magnetotransport properties is of pivotal importance, particularly in case of low-dimensional CoSi thin films and devices. Here we comprehensively investigate the magnetotransport and magnetic properties of ≈25 nm Co1-xSixthin films grown on a MgO substrate with controlled film microstructure (amorphous vs textured) and chemical composition (0.40 < x < 0.60). The resistivity of Co1-xSixthin films is nearly insensitive to the film microstructure and displays a progressive evolution from metallic-like (dρxx/dT > 0) to semiconducting-like (dρxx/dT < 0) regimes of conduction upon increasing the silicon content. A variety of anomalies in the magnetotransport properties, comprising for instance signatures consistent with quantum localization and electron-electron interactions, anomalous Hall and Kondo effects, and the occurrence of magnetic exchange interactions, are attributable to the prominent influence of intrinsic structural and chemical disorder. Our systematic survey brings to attention the complexity and the challenges involved in the prospective exploitation of the topological chiral semimetal CoSi in nanoscale thin films and devices.