New advanced fuel cell technologies are moving towards high-temperature proton conductors (HTPCs) to meet environmental issues. Their elaboration remains a challenge and micro-computed tomography (µCT) is an innovative way to control their quality. NiO-BZY anodic supports of a protonic ceramic electrochemical cell (PCEC), elaborated by co-tape casting and co-sintered at 1350 °C, were coated with a BZY20 electrolyte layer by DC magnetron sputtering. The µCT allowed to observe defects inside the volume of these PCEC half-cells and to show their evolution after an annealing treatment at 1000 °C and reduction under hydrogen. This technique consists in obtaining a 3D reconstruction of all the cross-sectional images of the whole sample, slice by slice. This allows seeing inside the sample at any desired depth. The resolution of 0.35 µm is perfectly adapted to this type of problem considering the thickness of the different layers of the sample and the size of the defects. Defects were detected, and their interpretation was possible thanks to the 3D view, such as the phenomenon of NiO grain enlargement explaining defects in the electrolyte, the effect of NiO reduction, and finally, some anomalies due to the shaping process. Ways to anticipate these defects were then proposed.