Complex oxide heterostructures provide access to emergent functional and structural phases which are not present in the bulk constituent materials. In this Rapid Communication, we focus on La0.67Sr0.33CoO3 (LSCO)/Gd heterostructures due to the high oxygen ion conductivity, as well as the coupled magnetic and electronic properties of LSCO, which are strongly dependent on the oxygen stoichiometry. This combination of properties enables the ionic control of the functional properties of LSCO thin films through the presence of oxygen getter layers such as Gd. We utilize X-ray nanodiffraction to directly image the nanoscale morphology of LSCO thin films as they are progressively transformed from the equilibrium perovskite phase to the metastable brownmillerite (BM) phase with increasing Gd thickness. Our studies show the coexistence of perovskite and BM phases with a critical oxygen vacancy concentration threshold which leads to the formation of extended BM filaments. In addition to lateral phase separation, we observed phase separation within the film thickness possibly due to pinning of the perovskite and BM phases by the substrate/LSCO and LSCO/Gd interface, respectively. Our studies provide a nanoscale survey of the phase separation in the cobaltites and shed light on the formation of the metastable BM phase.