Furandicarboxylate-based polyesters are considered an interesting class of bio-based polymers due to their improved properties with respect to the petrol-based terephthalate homologs. An in-depth analysis of the crystal structure of poly(propylene 2,5-furandicarboxylate) (PPF), after maximum possible removal of the catalyst, was carried out. The study disclosed that purified PPF presents two different crystalline phases after crystallization from the melt. Crystallizations at temperatures lower than 120 °C lead to growth of a single crystal form (β-form), whereas two different crystal forms (α and β) were found to coexist at higher Tcs. This behavior is opposite to that previously observed for unpurified PPF. The possibility that the catalyst nucleates the α-phase, which therefore becomes the kinetically favored modification at low crystallization temperatures in the presence of a higher amount of catalyst residue, has been considered as a feasible explanation. Two concomitantly different spherulitic morphologies were observed and connected to the β- and α-phase, respectively. The association between polymorphism and melting behavior was studied. The origin of the peaks that compose the multiple melting endotherm recorded at conventional heating rates was determined by combined wide-angle X-ray scattering, differential scanning calorimetry, fast scanning chip calorimetry, and polarized light optical microscopy measurements. The higher thermal stability of the α-crystals in comparison with the β-form was thus demonstrated.