In the present paper, a novel method to fabricate ordered arrays of Au/NiO/Au nanowires is described, with the aim of filling the gap between the fundamental study of the electrical properties of scattered single nanowires and the engineered fabrication of nanowire arrays. This approach mainly consists of the following steps: (a) electrodeposition of Au/Ni/Au nanowires into an ordered porous anodic aluminum oxide template; (b) mechanical polishing of the sample to expose the gold tips of Au/Ni/Au nanowires to the template surface; (c) in situ annealing of the Au/Ni/Au nanowires without removing the template. The resulting structure consists in an ordered array of Au/NiO/Au nanowires slightly protruding out of a flat aluminum oxide template. Unlike current approaches, with the described method it is not necessary to remove the template in order to oxidize the middle metal, thus allowing the availability of an entire set of metal/oxide/metal nanowires ordered in a two-dimensional matrix and where single heterojunctions can be accessed individually.