A distributed charge transfer (DCT) model has been developed to analyze solid oxide fuel cells (SOFCs) and electrolyzers operating in H2–H2O and CO–CO2 atmospheres. The model couples mass transport based on the dusty-gas model (DGM), ion and electron transport in terms of charged species electrochemical potentials, and electrochemical reactions defined by Butler–Volmer kinetics. The model is validated by comparison to published experimental data, particularly cell polarization curves for both fuel cell and electrolyzer operation. Parametric studies have been performed to compare the effects of microstructure on the performance of SOFCs and solid oxide electrolysis cells (SOECs) operating in H2–H2O and CO–CO2 gas streams. Compared to the H2–H2O system, the power density of the CO–CO2 system shows a greater sensitivity to pore microstructure, characterized by the porosity and tortuosity. Analysis of the pore diameter concurs with the porosity and tortuosity parametric studies that CO–CO2 systems are more sensitive to microstructural changes than H2–H2O systems. However, the concentration losses of the CO–CO2 system are significantly higher than those of the H2–H2O system for the pore sizes analyzed. While both systems can be shown to improve in performance with higher porosity, lower tortuosity, and larger pore sizes, the results of these parametric studies imply that CO–CO2 systems would benefit more from such microstructural changes. These results further suggest that objectives for tailoring microstructure in solid oxide cells (SOCs) operating in CO–CO2 are distinct from objectives for more common H2-focused systems.