Diffusion barrier composite films based on MFC and clay were developed with attention paid to the influence of thermal annealing and a fluorine-free silylation on their microstructure, water contact angle (WCA), mechanical properties, oxygen transmission rate (OTR) and water vapor transmission rate (WVTR). The MFC film without clay was hydrophilic with an OTR at 23°C that was highly dependent on relative humidity, increasing from 1.2 cm3/m2/day and 50%RH to 25.3 cm3/m2/day/bar at 80%RH. Annealing at 150ºC increased the crystallinity, the roughness and hydrophobicity of the film, with a WCA value of 86.4°, while decreasing its OTR at 80%RH by 20%. The addition of 10 wt% of clay did not impact the MFC structure and led to a 30% decrease of OTR at 80%RH due to a partial exfoliation, and to a 50% decrease when combined with annealing. Silylation increased the hydrophobicity of the film with a WCA of 127.5°, and its combination with clay and annealing led to a WCA of 146.5°, close to the superhydrophobic threshold of 150°. Silylation was the only treatment, which had a significant impact on the stiffness of the film, with a 10–20% decrease at low temperature for the different cases investigated (from ca. 6.3 GPa for untreated films to ca. 5.3 GPa for treated films), and a stable behavior up to 150ºC for the heat-treated film. The combination of clay, annealing and silylation considerably reduced the OTR at 80%RH to a value of 8 cm3/m2/day/bar, and the WVTR at 23°C and 50%RH from 49 g/m2/day for MFC to 22 g/m2/day. The reduction of OTR and WVTR was found to correlate with the increase in hydrophobicity of the film, which was attributed to the reduced access of water molecules within the MFC network.