This work illustrates that a variety of nanowire microstructures can be obtained either by controlling the nanowire formation kinetics or by suitable thermal processing of as-deposited nanowires with nonequilibrium metastable microstructure. In the present work, 200-nm diameter Ag–Ni nanowires with similar compositions, but with significantly different microstructures, were electrodeposited. A 15 mA deposition current produced nanowires in which Ag-rich crystalline nanoparticles were embedded in a Ni-rich amorphous matrix. A 3 mA deposition current produced nanowires in which an Ag-rich crystalline phase formed a backbone-like configuration in the axial region of the nanowire, whereas the peripheral region contained Ni-rich nanocrystalline and amorphous phases. Isothermal annealing of the nanowires illustrated a phase evolution pathway that was extremely sensitive to the initial nanowire microstructure.