In this research, we investigate the connection between an observed enhancement in solid oxide fuel cell stack performance and the evolution of the microstructure of its electrodes. A three dimensional, numerical model is applied to predict the porous ceramic-metal electrode performance on the basis of microstructure morphology. The model features a non-continuous computational domain based on the digital reconstruction obtained using focused ion beam scanning electron microscopy (FIB-SEM) electron nanotomography. The Butler–Volmer equation is used to compute the charge transfer at reaction sites, which are modeled as distinct locally distributed features of the microstructure. Specific material properties are accounted for using interpolated experimental data from the open literature. Mass transport is modeled using the extended Stefan–Maxwell model, which accounts for both the binary, and the Knudsen diffusion phenomena. The simulations are in good agreement with the experimental data, correctly predicting a decrease in total losses for the observed microstructure evolution. The research supports the hypothesis that the performance enhancement was caused by a systematic change in microstructure morphology.