Correlating nanostructure and optical properties of thin hybrid films is the crucial ingredient for designing sustainable applications ranging from structural colors in anticounterfeiting to sensors. Here, the tailoring of the refractive index of hybrid cellulose nanofibril/water-dispersed colloidal ink thin films is presented. The authors apply scalable, layer-by-layer slot-die coating for preparing the cellulose nanofibril and hybrid thin films. Making use of the mobility of the polymer chains in the colloids upon annealing, the influence of the different colloid sizes and their glass transition temperature on the refractive index of the hybrid material is shown. The complex refractive indices of the thin films are characterized by spectroscopic ellipsometry and correlated to the different nanostructures of the thin films. The authors find that post-deposition annealing changes the colloidal nanostructure from particulate to agglomerates. Depending on the size of the colloids, imbibition of the colloids into the cellulose nanofibril template is observed. This scalable approach offers new avenues in structural color functional biomaterial hybrid layers.