In this report, we present the synthesis of heterojunction magnetite nanowires in alumina template and describe magnetic and electrical properties from a single nanowire device for spintronics applications. Heterojunction Au-Fe-Au nanowire arrays were electrodeposited in porous aluminum oxide templates, and an extensive and controlled heat treatment process converted Fe segment to nanocrystalline cubic magnetite phase with well-defined Au-Fe3O4 interfaces as confirmed by the transmission electron microscopy. Magnetic measurements revealed Verwey transition shoulder around 120 K and a room temperature coercive field of 90 Oe. Current–voltage (I-V) characteristics of a single Au-Fe3O4-Au nanowire have exhibited Ohmic behavior. Anomalous positive magnetoresistance of about 0.5% is observed on a single nanowire, which is attributed to the high spin polarization in nanowire device with pure Fe3O4 phase and nanocontact barrier. This work demonstrates the ability to preserve the pristine Fe3O4 and well defined electrode contact metal (Au)–magnetite interface, which helps in attaining high spin polarized current.