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The synthesis, crystallization and subsequent phase separation of amorphous FeNiP in nanosized confinement is studied. Porous anodic aluminum oxide (AAO) could be utilized to control the regularity and shape of nanostructures via electrodeposition of amorphous FeNiP into the pores. An electrodeposited FeNiP film is analyzed as a reference system. Upon in situ annealing in the transmission electron microscope (TEM), the microstructural evolution is investigated. Calorimetry of the film shows a glass transition and crystallization which leads to a coarse grained structure. Crystallization of the nanowires yields a multilayered nanostructure, followed by a phase separation of FeNiP in multilayers of FeNi and FeNiP phases with interfaces perpendicular to the wire axis. Magnetic properties of the nanowire arrays have been analyzed using a Vibrating Sample Magnetometer (VSM).