Hydrogenation of double CC bonds is a valuable approach in organic synthesis. At the same time, selective hydrogenation of compounds with two or more similar CC bonds is a challenging task, since the process usually occurs at all available reaction centres simultaneously. In this work, selective hydrogenation of vinyl ethers with two and three CC bonds was successfully carried out using NaBH4as a hydrogen source in the presence of Ni and Co-based catalysts. The regioselectivity of the process depended on the method of catalyst generation under hydrogenation conditions. A one-step procedure with in situ catalyst generation resulted in non-selective hydrogenation of both C–CC and O–CC bonds, and a two-step procedure with a catalyst pre-treatment technique provided predominantly the products of O–CC bond hydrogenation. 14 polyunsaturated compounds were successfully hydrogenated using both proposed approaches, obtaining the target products in up to 98% yields. Using NMR spectroscopy and mass spectrometry, it was shown that under the procedure in 2 steps, hydrogenation occurred involving O–CC bond, while C–CC bond remained uninvolved. According to SEM and XRD analyses, metallic Ni and Co catalysts were formed from various initial Me2+compounds under the reaction conditions.