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Poly(ethylene 2,5-furandicarboxylate) (PEF) nanocomposites reinforced with Graphene nanoplatelets (GNPs) and Carbon nanotubes (CNTs) were in situ synthesized in this work. PEF is a biobased polyester with physical properties and is the sustainable counterpart of Polyethylene Terephthalate (PET). Its low crystallizability affects the processing of the material, limiting its use to packaging, films, and textile applications. The crystallization promotion and the reinforcement of PEF can lead to broadening its potential applications. Therefore, PEF nanocomposites reinforced with various loadings of GNPs, CNTs, and hybrids containing both fillers were prepared, and the effect of each filler on their structural characteristics was investigated by X-ray Diffraction (XRD), Fourier transform infrared spectroscopy—attenuated total reflectance (FTIR–ATR), and X-Ray Photoelectron Spectroscopy (XPS). The morphology and structural properties of a hybrid PEF nanocomposite were evaluated by Transmission Electron Microscopy (TEM). The thermo-oxidative degradation, as well as lifetime predictions of PEF nanocomposites, in an ambient atmosphere, were studied using Thermogravimetric Analysis (TGA). Results showed that the fillers’ incorporation in the PEF matrix induced changes in the lamellar thickness and increased crystallinity up to 27%. TEM analysis indicated the formation of large CNTs aggregates in the case of the hybrid PEF nanocomposite as a result of the ultrasonication process. Finally, the presence of CNTs caused the retardation of PEF’s carbonization process. This led to a slightly longer lifetime under isothermal conditions at higher temperatures, while at ambient temperature the PEF nanocomposites’ lifetime is shorter, compared to neat PEF.