Poly(alkylene 2,5-furanoate)s are considered as the most attractive and interesting alternatives to replace oil-based terephthalic polymers. These furan-based polyesters can be synthesized using fully bio-based synthetic strategies, allowing to reduce the environmental impact of plastics. At the same time, these polymers have shown outstanding thermal, mechanical and gas-barrier properties. All these results envisage their industrial use in the near future. Now, considering the downscaling of the products’ size towards the nanometer scale, we present a study of the morphology and nanomechanical properties of poly(alkylene 2,5-furanoate) thin films. Using Atomic Force Microscopy, we report the development of nanostructures upon crystallization, following different thermal treatments, for thin films with thicknesses below 200 nm. Moreover, we studied the impact of crystal growth in the nanomechanical properties of these materials. We found that the polymer thin films preserve their excellent mechanical response even in the confined geometry, as proved by the Young’s moduli values close to the GPa, accompanied by high surface stiffness, and low indentation depths. The poly(alkylene 2,5-furanoate) thin films were found to have nanomechanical properties comparable to those of the oil-based poly(ethylene terephthalate), a further evidence that in the future they could replace traditional polymers in several applications.