Changes in the local conformations of poly(ethylene 2,5-furandicarboxylate) (PEF) and poly(ethylene terephthalate) (PET) after crystallization from the amorphous state were studied and compared by infrared analysis. Both strain-induced crystallization (SIC) under uniaxial loading (D-PEF and D-PET) and crystallization under static conditions (TC-PEF and TC-PET) were used to determine the effect of mechanical stretching. It appears that, although the crystalline systems are the same, the inner organization of the amorphous phases is influenced by stretching. In addition to the increased incidence of the more extended aliphatic chain conformation (trans), stretching appears to reduce the number of activated hydrogen bonds between segments, which are more constrained in PEF than in PET. The effect of stretching on the beta-relaxation, which is related to local motions of carbonyl groups, showed that PEF carbonyl groups of amorphous regions are freed by the stretching. We conclude that the different chain architectures of the polyesters induce different sensitivities of the amorphous phase to the drawing process.