After successful preparation of master batch formulations including polyhydroxybutyrate (PHB) and fibrillated cellulose additives, the compositions with different types and concentrations of fillers were used for the deposition of a coating on packaging paper grades, by using compression moulding in a hydraulic press. The resulting paper coatings are considered to provide a green solution for the production of protective barrier layer films with tunable hydrophobicity and oxygen barrier resistance. The processing of the nanocomposites into flat and homogeneous coatings was optimized for different conditions of moulding temperature and times, in particular, the flow conditions of the coating under pressing in contact with the substrate strongly depends on the presence of fillers. The effects of filler types on adhesion of the coating at the paper/polymer interface were investigated and the poor adhesion of native PHB coatings was tremendously improved after hydrophobic surface modification of the nanocellulose fillers. The inclusion of a wax and nanoparticles attached to the nanocellulose fiber surface enhanced the flowing properties of the coating by eliminating fiber agglomeration in contact with the paper substrate and reducing the effects of fiber pull outs. Therefore, hydrophobic fiber modification is necessary to obtain a homogenous dispersion during compressing moulding of coating materials for paper applications. Furthermore, the effect of processing on the final crystallinity of the master batches, films and paper coatings is presented by considering the reduction in degree of crystallinity for coatings in contact with a paper substrate owing to the surface confinement of crystallization processes. On the other hand, also the time-effects of secondary crystallization of the coatings as a function of aging time were lower for the coatings as compared to the free-standing films, in relation with the reduction of molecular mobility of the polymer chains under confined conditions.