The purpose of this work was to carry out comparative studies of WC-Co-Cr coatings deposited using the high velocity oxy fuel (HVOF) method onto two types of substrate material: structural steel S235 and magnesium alloy AZ31. The influence of the substrate material type on the microstructure, phase composition, crystallite size, porosity, Vickers microhardness, instrumental hardness (HIT), Young’s modulus (EIT), and fracture toughness was investigated. For both substrates, the deposited coatings deposited were characterized with fine-grained and compact microstructure. The X-ray diffraction (XRD) revealed presence of following phases: WC, W2C, Co0.9W0.1, and Co3W9C4. The WC phase was the most desirable and stable one with crystallites were below 100 nm. On the other hand, the size of the W2C crystallites was below 30 nm. The coatings obtained showed porosity values equal to 2.3 ± 0.4 vol% and 2.8 ± 0.7 vol% for AZ31 and S235, respectively. The average Vickers microhardness for both types of sample was appproximately 1200 HV0.3. The average HIT values for carbide particles and metallic matrix were around 29 GPa and 6.5 GPa, respectively. In the case of EIT, it was around 620 GPa and 190 GPa for WC and Co-Cr, respectively. The differences between coatings were negligible. The EIT value for both coatings was equal to 344 ± 11 GPa. The fracture toughness was around 4.5 MPa · m1/2 in both cases. The investigations revealed that it is possible to replace steel substrate material with a much lighter equivalent, in this case AZ31 alloy, without deterioration of the coating properties.