As awareness of the environmental impact of fossil‐based polymers grows, the demand for biobased alternatives rises. In this context, combining eco‐friendly synthesis techniques with renewable resources is important to produce polymers efficiently and sustainably. Furandicarboxylic acid (FDCA) is one of the key building blocks for producing biobased polymers. However, most studies predominantly focus on 2,5‐FDCA, while FDCA encompasses other noteworthy isomers, namely, 2,4‐ and 3,4‐FDCA. The polymers derived from these two isomers have recently gained attention due to their promising properties. In this study, an environmentally friendly approach for producing biobased polyesters from 2,5‐, 2,4‐, and 3,4‐FDCA dimethyl ester isomers is proposed. The synthesis is conducted under greener conditions, utilizing Candida antarctica lipase B (CALB) enzyme as a biocatalyst. The performance of the enzyme is assessed, revealing CALB preference for polymerizing 2,5‐FDCA over 2,4‐ and 3,4‐FDCA dimethyl ester, which is elucidated by docking analysis. Moreover, CALB shows varying rates of cyclic oligomer formation for each isomer, favoring 2,5‐FDCA cyclization. The structure‐property relationship, encompassing the variation in isomeric structure, is evaluated through structural characterization, thermal analysis, and surface properties. This study primarily emphasized enzymatic polymerization and highlighted its versatility in accommodating different monomer isomeric substitutions.