Dual phase oxide membranes have shown promising hydrogen permeation fluxes in syngas applications due to their high mixed proton electron conduction (MPEC). However, the conductivity of grain boundaries can be many orders of magnitude lower than that of the bulk and so limits the total conductivity and hydrogen permeation. In this study, the three‐dimensional nanoscale oxygen and cation distributions around grain and phase boundaries in a BaCe0.8Y0.2O3‐δ‐Ce0.8Y0.2O2‐δ (BCY‐YDC) membrane were quantified by atom probe tomography (APT) and related to average grain boundary conductivity measured by electrochemical impedance spectroscopy (EIS). Segregation varied among the general high‐angle grain boundaries analyzed, but no trend from orientation analysis was determined. Correlative APT and electron energy loss spectroscopy (EELS) of one YDC grain boundary revealed composition and cerium valence information, respectively, allowing for the determination of vacancies at the grain boundary. While a specific MPEC membrane is characterized, the results are relevant to proton and electron conduction in a number of technologically important ceramics.