The article describes the effect of heat treatment on the structural-phase state and properties of a multilayer Cr-Al-Co-Y coating obtained by magnetron sputtering. Heat treatment was carried out at 400, 800 and 1000 °C. The study of the microstructure was carried out by electron microscopy with energy dispersive analysis and powder X-ray diffraction. The surface of the samples was studied by atomic force microscopy. The thickness of the Co-Cr-Al-Y coatings was 1.5–1.7 ± 0.2 µm. The obtained coatings are characterized by a hardness of 4.7–6.4 GPa. A distinctive feature of the layers is the absence of a crystalline structure in some areas of the coating. The main process occurring during the thermal treatment is the formation of a spinel-type phase. For a single-layer sample after heat treatment at 400 °C, it was not possible to fix extraneous reflections except for the reflections of the silicon substrate 111 and 220. For the rest of the samples, the appearance of reflections of a number of phases was noticed, such as: SiO2, CoO, AlSi0.5O2.5 and CrAl0.42Si1.58. An increase in the treatment temperature up to 800 °C did not lead to significant changes. In the case of the multilayer sample, the reflections of various impurity phases disappeared and the Co3O4 phase was formed. For samples treated at 1000 °C, the formation of a spinel-type phase (Co3O4-CoCr2O4) was observed in all cases. Data on the structural-phase state and properties of the multilayer Co-Cr-Al-Y coating can be used to predict the nature of such coatings after heat treatment.