Perovskite phase instability of BiMnO3 has been exploited to synthesize epitaxial metal oxide magnetic nanocrystals. Thin film processing conditions are tuned to promote the breakdown of the perovskite precursor into Bi2O3 matrix and magnetic manganese oxide islands. Subsequent cooling in vacuum ensures complete volatization of the Bi2O3, thus leaving behind an array of self-assembled magnetic Mn3O4 nanostructures. Both shape and size can be systematically controlled by the ambient oxygen environments and deposition time. As such, this approach can be extended to any other Bi-based complex ternary oxide system as it primarily hinges on the breakdown of parent Bi-based precursor and subsequent Bi2O3 volatization.