In this study, poly(ethylene 2,5-furan dicarboxylate) (PEF) was synthesized from biomass-based dimethyl furan-2,5-dicarboxylate using different-sized zeolites, with substituted ions such as Li and K, as efficient green catalysts for in situ polymerization. The Z5Ali catalyst yielded the PEF biopolyester with the highest weight-average molecular weight among all the samples: 53,800 g/mol. From their TGA curves, it was confirmed that the PEF sample with ZA5Li as the catalyst showed an increased thermal stability compared to homo-PEF. Generally, homo-PEF exhibited a very low melt-crystallization rate with low enthalpy. However, all the PEF samples using zeolite as the catalyst formed endotherms I and II. This result was attributed to the fact that zeolite affects the melt and recrystallization of imperfect crystals due to physical hindrance.