Cellulose Nanocrystals, CNC, opportunely functionalized are proposed as reactive fillers in bio-based flexible polyurethane foams to improve, mainly, their mechanical properties. To overcome the cellulose hydrophilicity, CNC was functionalized on its surface by linking covalently a suitable bio-based polyol to obtain a grafted-CNC. The polyols grafted with CNC will react with the isocyanate in the preparation of the polyurethane foams. An attractive way to introduce functionalities on cellulose surfaces in aqueous media is silane chemistry by using functional trialkoxy silanes, X-Si (OR)3. Here, we report the synthesis of CNC-grafted-biopolyol to be used as a successful reactive filler in bio-based polyurethane foams, PUFs. The alkyl silanes were used as efficient coupling agents for the grafting of CNC and bio-polyols. Four strategies to obtain CNC-grafted-polyol were fine-tuned to use CNC as an active filler in PUFs. The effective grafting of the bio polyol on CNC was evaluated by FTIR analysis, and the amount of grafted polyol by thermogravimetric analysis. Finally, the morphological, thermal and mechanical properties and hydrophobicity of filled PUFs were thoughtfully assessed as well as the structure of the foams and, in particular, of the edges and walls of the cell foams by means of the Gibson–Ashby model. Improved thermal stability and mechanical properties of PU foams containing CNC-functionalized-polyol are observed. The morphology of the PU foams is also influenced by the functionalization of the CNC.