One of the greatest goals of modern polymer science can be considered the production of high-performance polymer nanocomposites from renewable sources due to the growing interest in environmental and sustainability issues. Within that scope, a good strategy is to pair the processability of thermoplastic materials with the outstanding characteristics of 2D nanomaterials. However, the final performance of the produced nanocomposite is mainly attributed to the interphase, i.e., the volume fraction of the bulk polymer that has its molecular dynamics affected by interactions with the surface of the filler. Therefore, we aim to investigate how different 2D nanomaterials, i.e., graphene oxide (GO), hexagonal-boron nitride (h-BN), and molybdenum disulfide (MoS2) affect the molecular dynamics of a fully bio-based polyamide 1010 (PA 1010) by a new correlation between experimental results from differential scanning calorimetry, broadband dielectric spectroscopy, and dynamic mechanical analysis. For that, nanocomposites based on single and hybrid-fillers were produced through melt mixing. It was observed that, although all nanofillers seem to hinder the molecular relaxation of the polymer chains, GO and h-BN were more effective than MoS2. This remained true when the fillers were applied individually and in the hybrid form. This effect has been attributed to the following aspects: (I) higher enthalpy related to the melting of the polyamide crystals after the Brill transition, which indicates lower thermal motion being gained before the transition takes place; (II) higher activation energy of the glass transition, which was estimated from the fitting of the dielectric spectra to the Havriliak-Negami function and then to the Vogel-Fulcher-Tammann model; (III) lower values of the “adhesion factor”, which is calculated from the decrease in intensity of the mechanical tan(δ) in the nanocomposites with respect to the neat polymer, indicating higher adhesion for the composites filled with GO and h-BN. To confirm the trends observed experimentally for each nanomaterial, molecular dynamics simulations, which enabled the investigation of the adhesion force as a function of nanosheet displacement, were also carried out. The simulations corroborated with the experimental observations, in which h-BN leads to a more intense force of separation, followed by GO, and lastly by MoS2. Since the level of interfacial interactions is what mainly dictates the performance of polymer nanocomposites, it is suggested that GO, and especially h-BN, might present greater promise for novel bionanocomposites based on PA 1010.