Fabrication of thin film nanocomposites via decomposition and self-assembly from the vapor phase is a promising path for cost-effective fabrication of multifunctional materials. In particular, oxides as a new class of energy materials allow for rich functionalities, e.g., by combining p- and n-doped systems in catalytic or light harvesting units. Combining A-site doped perovskites ABO3 with CoFe2O4 spinel, we have investigated thin film phase composition and nanocomposite morphology in the pseudobinary system La0.6Sr0.4BO3–CoFe2O4 for B = Fe, Co, and Mn. We observe formation of an epitaxial two-phase nanocomposite for B = Fe, i.e., the coexistence of La0.6Sr0.4FeO3 and CoFe2O4. In contrast, for B = Co or Mn nanocomposites are formed, where perovskite La0.6Sr0.4BO3 solid solutions coexists with Co-rich spinel and periclase phases. We derive conclusions for the preparation of perovskite-spinel nanocomposites with well-designed doping levels.