The effects of long-term operation in electrolysis mode on the microstructure of Ni/YSZ electrodes were investigated. The electrode structures were investigated in “as reduced” state and after 9000 h of operation in a 25 cell stack. Microstructural data were obtained by scanning electron microscopy and focused-ion-beam serial sectioning. Microstructural characteristics were extracted by 1D and 3D methods. Significant microstructural changes were observed between the two cells analyzed. A significant loss of Ni in the active electrode is observed, from ~ 29% (by volume) in the reference cell to ~ 24% as well as a coarsening of the Ni particle sizes. The long-term tested cell shows lower percolating triple phase boundary density (0.76 µm/µm3) than the un-tested reference (2.0 µm/µm3). This reduction is mainly due to the loss of triple phase boundary percolation through the Ni phase where a reduction from a percolation degree above 90% to ~50% is observed.