The thin film electrolyte known as Lipon (lithium phosphorous oxynitride) has proven successful for planar thin film battery applications. Here, the sputter deposition of the amorphous LiPON electrolyte onto more complex 3D structures is examined. The 3D structures include off-axis alignment of planar substrates and also 10–100 μm arrays of pores, columns, and grooves. For magnetron sputtering in N2 gas at 2.6 Pa, the Lipon film deposition is not restricted to be line-of-sight to the target, but forms conformal and dense films over the 3D and off-axis substrates. The deposition rate decreases for areas and grooves that are less accessible by the sputtered flux. The composition varies, but remains within the range that gives sufficient Li+ ionic conductivity, 2 ± 1 μS/cm.