The excessive use of petroleum-based plastic packaging has raised concerns about its environmental impacts, leading to research on sustainable and economically viable biopolymer-based nanocomposites. However, there are still challenges related to the intrinsic characteristics of some biopolymers that differ substantially from conventional polymers, in terms of mechanical properties and water affinity. To address these issues, natural rubber (NR) latex coated with cellulose nanocrystals (CNCs) composites were explored as an effective alternative to tuning up physical properties of biopolymers. The deposition of CNCs on NR surface was innovatively devised through the utilization of the freeze-drying method, employing a green approach that eliminates the need for organic solvents. The NR coated with CNCs was incorporated into the starch matrix, varying the nanofiller mass percentage in the biopolymer (2, 5, and 10 wt%), the NR content in the nanofiller (0, 1, and 5 wt%), and the nanofiller preparation method (liquid nitrogen – N and gradual freezing – F). All starch-based films demonstrated notable transparency to visible light, and the incorporation of CNC/NR from N led to a reduction of 28 % in water vapor transmission rate compared to starch with glycerol, aligning with the filler percentage in the matrix. The addition of CNC/NR contributed to an increase of 76 % in the tensile strength and 53 % in the Young’s modulus of the bionanocomposites compared to starch with glycerol. Notably, the freeze-drying method allowed for the compatibilization of NR with a hydrophilic matrix without compromising the mechanical properties of starch-based bionanocomposites. Furthermore, films containing the CNC/NR nanofillers assisted in delaying the ripening of fresh-cut bananas, in addition to accelerating the biodeterioration of starch-based films. These findings indicate a promising avenue for the development of a new generation of green nanofillers that can be conveniently hydrophobically tailored to suit carbohydrate polymeric matrices.