The colloidal layer formation on porous materials is a crucial step for printing and applying functional coatings, which can be used to fabricate anticounterfeiting paper. The deposition of colloidal layers and subsequent thermal treatment allows for modifying the hydrophilicity of the surface of a material. In the present work, wood-based colloidal inks are applied by spray deposition on spray-deposited porous cellulose nanofibrils (CNF) films. The surface modification by thermal annealing of the fabricated colloid-cellulose hybrid thin films is investigated in terms of layering and hydrophobicity. The polymer colloids in the inks are core-shell nanoparticles with different sizes and glass transition temperatures (T-g), thus enabling different and low thermal treatment temperatures. The ratio between the core polymers, poly(sobrerol methacrylate) (PSobMA), and poly(-butyl methacrylate) (PBMA) determines the T-g and hence allows for tailoring of the T-g. The layer formation of the colloidal inks on the porous CNF layer depends on the imbibition properties of the CNF layer which is determined by their morphology. The water adhesion of the CNF layer decreases due to the deposition of the colloids and thermal treatment except for the colloids with a size smaller than the void size of the porous CNF film. In this case, the colloids are imbibed into the CNF layer when T-g of the colloids is reached and the polymer chains transit in a mobile phase. Tailored aggregate and nanoscale-embedded hybrid structures are achieved depending on the colloid properties. The imbibition of these colloids into the porous CNF films is verified with grazing incidence small-angle X-ray scattering. This study shows a route for tuning the nanoscale structure and macroscopic physicochemical properties useful for anticounterfeiting paper.