Vertically aligned nanocomposites (VANs) are unique thin films with vertical nanostructures embedded in a matrix material, allowing for the integration of two distinct materials. These nanocomposites offer novel combined physical properties, such as nanocomposite-based multiferroics and strongly coupled physical properties, such as magneto-optic coupling. Much work has been conducted in exploring different two-phase combinations and various processing conditions to achieve novel tunable properties that cannot be obtained by any single-phase material alone. In this work, the target configuration effects are explored for the growth of LaFeO 3 −CoNi 2 O 4 VANs. Both mixed and pie-shaped targets are utilized to compare the target configuration effects on the phase separation, morphology tuning, and their resulting physical properties, including optical and magnetic properties. This work suggests that the target configuration is another important parameter for achieving the desired VAN morphology and can be used to design different two-phase VANs with tailorable properties.