Flow hydrogenation performed over heterogeneous catalysts makes organic synthesis more economical, safe and environmentally friendly. Over the past two decades, a significant amount of research with a major focus on noble metal catalysts has been carried out in this area. However, catalysts based on non-noble metals (Ni, Cu, Co, etc.) are more promising for practical use due to their low cost and high availability. This review article discusses the use of supported and bulk non-noble metal catalysts for the liquid-phase hydrogenation of bi- and polyfunctional organic compounds in flow mode. The main attention is paid to the selective reduction of one functional group (NO2, CC, CN, CO, and CN) in the presence of other substituents. In addition, cascade synthetic protocols involving hydrogenation are presented.