Three perylene diimides (PDI) were synthesized with propargyl groups at the diimide positions to enable the fabrication of molecular multilayer thin films via sequential copper(I) catalyzed azide-alkyne cycloaddition (CuAAC) coupling reactions in a layer-by-layer (LbL) fashion. The new PDIs with phenoxy (PhO-PDI), dodecylthiol (Thiol-PDI), and pyrrolidine (Pyrr-PDI) substituents in bay positions have optical absorption spectra that span a large portion of the visible region. Multilayer growth on 11-azidoundecylsiloxane coated silica glass and indium tin oxide (ITO) surfaces was demonstrated up to 10 bilayers of each PDI with 1,3,5-tris(azidomethyl)-benzene (N₃Mest) via optical and infrared spectroscopy. Polarized UV-visible absorption measurements showed a strong dependence on the orientation of the film in the light path and was consistent with a preferential orientation of the PDI molecules in the film at 40–42° with respect to the substrate surface. Grazing-angle attenuated total reflectance (GATR) infrared spectra of the films show an increase in content of unreacted azides during multilayer growth from N₃Mest as a result of the smaller molecular footprint as compared to the PDI components. Electrochemical scans of the multilayer films grown on ITO exhibited reversible two-electron reduction waves for the PDIs with linear increases in charge with bilayer growth. The electrochemically derived surface coverages of PDIs averaged 1.2–1.3 × 10¹⁴ molecules per cm² for each layer added to the multilayer films. The flexibility of the CuAAC based LbL assembly methodology is highlighted by the assembly of a mixed multilayer film containing five layers of each PDI, resulting in a panchromatic film that is a summation of individual chromophores.