In this paper, we report on the synthesis of FeCo/Cu multisegmented nanowires by means of pulse electrodeposition in nanoporous anodic aluminum oxide arrays supported on silicon chips.By adjusting the electrodeposition conditions, such as the pulse scheme and the electrolyte, alternating segments of Cu and ferromagnetic FeCo alloy can be fabricated. The segments can be built with a wide range of lengths (15 -150 nm) and exhibit a close-to-pure composition (Cu or FeCo alloy) as suggested by EDX mapping results. The morphology and the crystallographic structure of different nanowire configurations have been assessed thoroughly concluding that Fe, Co and Cu form solid solution. Magnetic characterization using vibrating sample magnetometry and magnetic force microscopy reveals that by introducing non-magnetic Cu segments within the nanowire architecture, the magnetic easy axis can be modified and the reduced remanence can be tuned to the desired values. The experimental results are in agreement with the provided simulations. Furthermore, the influence of nanowire magnetic architecture on the magnetically triggered protein desorption is evaluated for three types of nanowires: Cu, FeCo and multisegmented FeCo15 nm/Cu15 nm. The application of an external magnetic field can be used to enhance the release of proteins on-demand. For fully magnetic FeCo nanowires the applied oscillating field increased protein release by 83%, whereas this was found to be 45% for multisegmented FeCo15 nm/Cu15 nm nanowires. Our work suggests that a combination of arrays of nanowires with different magnetic configurations could be used to generate complex substance concentration gradients or control delivery of multiple drugs and macromolecules.