Cubic perovskites BaxSr1 − xCo0.8Fe0.2O3 − δ (BSCF) are among the most promising oxygen permeable membrane materials and high-performance cathode materials for intermediate temperature solid oxide fuel cells. Here, we show that cubic BSCF becomes unstable in air at intermediate temperatures and gradually transforms to a hexagonal perovskite on cooling. Cubic and hexagonal BSCF polymorphs were observed to coexist below 850–900 °C, and the amount of the hexagonal polymorph was shown to increase at the expense of the cubic polymorph with decreasing temperature. Different chemical composition of the two coexisting phases was inferred, but a complete transformation to the hexagonal polymorph was hindered by slow cation diffusion. Due to the sluggish kinetics, usual cooling rates lead to the meta-stable cubic BSCF, but over time the transition to the stable hexagonal polymorph may be detrimental to applications incorporating BSCF. We show that the transformation of the cubic to hexagonal polymorph of BSCF can be rationalized by the Goldschmidt tolerance factor and accordingly suppressed by appropriate substitutions.