Mixed conducting cobaltites PrBaCo2−xFexO6−δ (x = 0–0.6) with a double perovskite structure are promising materials for ceramic semi-permeable membranes for oxygen separation and purification due to their fast oxygen exchange and diffusion capability. Here, we report the results of the detailed study of an interplay between the defect chemistry, oxygen nonstoichiometry and oxygen transport in these materials as a function of iron doping. We show that doping leads to a systematic variation of both the thermodynamics of defect formation reactions and oxygen transport properties. Thus, iron doping can be used to optimize the performance of mixed conducting oxygen-permeable double perovskite membrane materials.