The aim of this study is to investigate the effect of yttrium-doped barium zirconate-cerate (BaZr0.3Ce0.5Y0.2O3−δ, BZCY) refinement on cell stability under operational fuel cell conditions. For this purpose, anode-supported cells, comprised of a nickel oxide (NiO)-BZCY anode, a BZCY electrolyte, and a BZCY-La0.6Sr0.4Co0.2Fe0.8O3−δ composite cathode are successfully prepared with refined or as-calcined BZCY powder. The long-term fuel cell performance is evaluated under a potentiostatic measurement at 600 °C. The cell with the refined BZCY electrolyte shows a modest power density of 47 mW cm−2 at a 600 °C operating temperature over 480 h without any significant performance loss, whereas the cell with the as-calcined BZCY electrolyte displays a rapid degradation of cell performance over 110 h. A post-testing analysis of the cell with the refined BZCY does not reveal any evidence of delamination resulting from electrolyte surface decomposition. These results demonstrate that the refinement process significantly enhances the chemical stability of BZCY-based proton conducting fuel cells, which produce a high content of water vapor on the cathode side.