Protonic ceramic fuel cells (PCFCs) offer a convenient means of converting chemical energy into electricity with high performance and efficiency at low- and intermediate-temperature ranges. However, in order to ensure good life-time stability of PCFCs, it is necessary to ensure rational chemical design in functional materials. Within the present work, we propose new Ni-based perovskite phases of PrNi0.4M0.6O3–δ (where M = Co, Fe) for potential utilization in protonic ceramic electrochemical cells. Along with their successful synthesis, functional properties of the PrNi0.4M0.6O3–δ materials, such as chemical compatibility with a number of oxygen-ionic and proton-conducting electrolytes, thermal expansion behavior, electrical conductivity, and electrochemical behavior, were comprehensively studied. According to the obtained data, the Co-containing nickelate exhibits excellent conductivity and polarization behavior; on the other hand, it demonstrates a high reactivity with all studied electrolytes along with elevated thermal expansion coefficients. Conversely, while the iron-based nickelate had superior chemical and thermal compatibility, its transport characteristics were 2–5 times worse. Although, PrNi0.4Co0.6O3–δ and PrNi0.4Fe0.6O3–δ represent some disadvantages, this work provides a promising pathway for further improvement of Ni-based perovskite electrodes.