Zinc oxide (ZnO) and porous anodic aluminum oxide (PAAO) are technologically important materials, rich with features that are of interest in optical applications, for example, in light-emitting and sensing devices. Here, we present synthesis method of aligned ZnO nanorods (NR) with 40 nm diameter and variable length in 150 to 500 nm range obtained by atomic layer deposition (ALD) of ZnO in pores of continuously variable thickness PAAO. The relative intensity of yellow (1.99 eV), green (2.35 eV), and blue (2.82 eV) photoluminescence (PL) components originating from the different types of defects, varied with non-monotonic dependency on the composite film thickness with a Fabry–Pérot like modulation. The intensity variation of any individual PL component correlated well with anti-reflective properties of ZnO NR–PAAO composite film at the peak wavelength of the particular PL component. This provides a route for selective enhancement or suppression of color components of hybrid fluorescent emitters by tuning only geometric parameters, with potential use in imaging and other optical devices. As an application example we tested the composite film for sensing of vascular endothelial growth factor (VEGF) using a widely accessible fluorescence microscopy setup. The intensity of the yellow and green PL components reduced in response to increased VEGF concentrations, whereas blue component remained invariant.