Reducing the effect of global warming and increasing the needs for fuel sources appoint hydrogen utilization in fuel cell technology a very promising demand. A step for required pure hydrogen production for this purpose is the water-gas shift (WGS) reaction and the design of well performing but cost effective WGS catalysts, the latter being of growing research interest. In the present study catalysts containing copper (3 wt%) supported on ceria/alumina (30 wt% ceria) and Y-doped ceria/alumina (1 wt% Y2O3 regarding ceria content) were prepared by impregnation (IM) and by mechanochemical mixing (MM). The effect of support synthesis methods on the performance in the WGS reaction was discussed based on catalyst characterization by means of XRD, HRTEM, XPS, and H2-TPR methods. It was established that the effect of Y-doping was strongly dependent on the method of support preparation being positive for MM and unfavourable in the case of impregnation. The IM method caused the formation of a superficial phase with CuO, Y-dopant, and ceria in close location. Additionally, a higher amount of oxygen vacancies was related to non-reducible Y3+ ions that interrupted Cu–oxygen vacancy–Ce interaction thus leading to both lower reducibility and WGS activity. The presence of yttria phase located on ceria-free alumina in the case of MM support decreased the negative influence of Ce3+ replacement by Y3+ ions. A positive effect of separate Y2O3 could explain the best WGS performance observed. Long-term WGS tests showed good stability thus making this catalyst promising composed mainly of alumina and low amount of active phases. The study contributes to the development of an advantageous formulation of well-performing and economically profitable WGS catalysts for efficient improving of hydrogen purity for small-scale applications.