Poly(ethylene furanoate) (PEF)-based nanocomposites were fabricated with silver (Ag) and titanium dioxide (TiO2) nanoparticles by the in-situ polymerization method. The importance of this research work is to extend the usage of PEF-based nanocomposites with improved material properties. The PEF-Ag and PEF-TiO2 nanocomposites showed a significant improvement in color concentration, as determined by the color colorimeter. Scanning electron microscopy (SEM) photographs revealed the appearance of small aggregates on the surface of nanocomposites. According to crystallinity investigations, neat PEF and nanocomposites exhibit crystalline fraction between 0–6%, whereas annealed samples showed a degree of crystallinity value above 25%. Combining the structural and molecular dynamics observations from broadband dielectric spectroscopy (BDS) measurements found strong interactions between polymer chains and nanoparticles. Contact angle results exhibited a decrease in the wetting angle of nanocomposites compared to neat PEF. Finally, antimicrobial studies have been conducted, reporting a significant rise in inhibition of over 15% for both nanocomposite films against gram-positive and gram-negative bacteria. From the overall results, the synthesized PEF-based nanocomposites with enhanced thermal and antimicrobial properties may be optimized and utilized for the secondary packaging (unintended food-contact) materials.