Poly(ethylene 2,5-furandicarboxylate) (PEF)-based nanocomposites containing Ce–bioglass, ZnO, and ZrO2 nanoparticles were synthesized via in situ polymerization, targeting food packaging applications. The nanocomposites were thoroughly characterized, combining a range of techniques. The successful polymerization was confirmed using attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, and the molecular weight values were determined indirectly by applying intrinsic viscosity measurements. The nanocomposites’ structure was investigated by depth profiling using time-of-flight secondary ion mass spectrometry (ToF-SIMS), while color measurements showed a low-to-moderate increase in the color concentration of all the nanocomposites compared to neat PEF. The thermal properties and crystallinity behavior of the synthesized materials were also examined. The neat PEF and PEF-based nanocomposites show a crystalline fraction of 0–5%, and annealed samples of both PEF and PEF-based nanocomposites exhibit a crystallinity above 20%. Furthermore, scanning electron microscopy (SEM) micrographs revealed that active agent nanoparticles are well dispersed in the PEF matrix. Contact angle measurements showed that incorporating nanoparticles into the PEF matrix significantly reduces the wetting angle due to increased roughness and introduction of the polar -OH groups. Antimicrobial studies indicated a significant increase in inhibition of bacterial strains of about 9–22% for Gram-positive bacterial strains and 5–16% for Gram-negative bacterial strains in PEF nanocomposite films, respectively. Finally, nanoindentation tests showed that the ZnO-based nanocomposite exhibits improved hardness and elastic modulus values compared to neat PEF.