Perovskite oxides are gaining significant attention for use in next-generation magnetic and ferroelectric devices due to their exceptional charge transport properties and the opportunity to tune the charge, spin, lattice, and orbital degrees of freedom. Interfaces between perovskite oxides, exemplified by La 1−x Sr x CoO 3−δ /La 1−x Sr x MnO 3−δ (LSCO/LSMO) bilayers, exhibit unconventional magnetic exchange switching behavior, offering a pathway for innovative designs in perovskite oxide-based devices. However, the precise atomic-level stoichiometric compositions and chemophysical properties of these interfaces remain elusive, hindering the establishment of surrogate design principles. We leverage first-principles simulations, evolutionary algorithms, and neural network searches with on-the-fly uncertainty quantification to design deep learning model ensembles to investigate over 50,000 LSCO/LSMO bilayer structures as a function of oxygen deficiency (δ) and strontium concentration (x). Structural analysis of the low-energy interface structures reveals that preferential segregation of oxygen vacancies toward the interfacial La 0.7 Sr 0.3 CoO 3−δ layers causes distortion of the CoO x polyhedra and the emergence of magnetically active Co 2+ ions. At the same time, an increase in the Sr concentration and a decrease in oxygen vacancies in the La 0.7 Sr 0.3 MnO 3−δ layers tend to retain MnO 6 octahedra and promote the formation of Mn 4+ ions. Electronic structure analysis reveals that the nonuniform distributions of Sr ions and oxygen vacancies on both sides of the interface can alter the local magnetization at the interface, showing a transition from ferromagnetic (FM) to local antiferromagnetic (AFM) or ferrimagnetic regions. Therefore, the exotic properties of La 1−x Sr x CoO 3−δ /La 1−x Sr x MnO 3−δ are strongly coupled to the presence of hard/soft magnetic layers, as well as the FM to AFM transition at the interface, and can be tuned by changing the Sr concentration and oxygen partial pressure during growth. These insights provide valuable guidance for the precise design of perovskite oxide multilayers, enabling tailoring of their functional properties to meet specific requirements for various device applications.