Multicomponent nanoparticles can be synthesized with either homogeneous or phase-segregated architectures depending on the synthesis conditions and elements incorporated. To understand the parameters that determine their structural fate, multicomponent metal-oxide nanoparticles consisting of combinations of Co, Ni, and Cu were synthesized via scanning probe block copolymer lithography and characterized using correlated electron microscopy. These studies revealed that the miscibility, ratio of the metallic components, and the synthesis temperature determine the crystal structure and architecture of the nanoparticles. A Co-Ni-O system forms a rock salt structure largely due to the miscibility of CoO and NiO, while Cu-Ni-O, which has large miscibility gaps, forms either homogeneous oxides, heterojunctions, or alloys depending on the annealing temperature and composition. Moreover, a higher ordered structure, Co-Ni-Cu-O, was found to follow the behavior of lower ordered systems.