A new azido functionalized 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) has been synthesized to achieve spectral complementarity to a Zn(II) tetraphenylethynyl porphyrin (ZnTPEP). Mixed multilayer films were assembled on glass and quartz up to 10 bilayers thick in a layer-by-layer (LbL) fabrication process using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) to couple these two dyes together with a tris-azido linker. By varying the amount of BODIPY in the CuAAC reaction solutions for the azido linker layers, we achieve tunable doping of BODIPY within the porphyrin films. We are able to demonstrate linear film growth and determine thickness by X-ray reflectivity (XRR). XRR data indicated that lower BODIPY loading leads to higher porphyrin content and slightly thicker films. Fluorescence emission and excitation spectra of the mixed multilayer films show efficient quenching of the BODIPY singlet and enhanced ZnTPEP emission, suggesting efficient energy transfer (EnT). The ease of fabrication and tunability of these films may serve as potential light harvesting arrays for molecular-based solar cells.