Here, we report a new two-step enzymatic polymerization strategy for the synthesis of poly(octamethylene suberate) (POS) using an immobilized Pseudozyma antarctica lipase B (IMM-PBLI). The strategy overcomes the lack of enzymatic POS synthesis in solvent-free systems and increases the final polymer molecular weight. In the first step, the direct polycondensation of suberic acid and 1,8-octanediol was catalyzed by IMM-PBLI at 45 °C, leading to the production of prepolymers with molecular weights (MWs) of 2800, 3400, and 4900 g mol−1 after 8 h in miniemulsion, water, and an organic solvent (cyclohexane: tetrahydrofuran 5:1 v/v), respectively. In the second polymerization step, wet prepolymers were incubated at 60 or 80 °C, at atmospheric pressure, in the presence of IMM-PBLI, and without stirring. The final POS polymers showed a significant increase in MW to 5000, 5800, and 19,800 g mol−1 (previously synthesized in miniemulsion, water, or organic solvent, respectively). FTIR analysis of the final polymers confirmed the successful POS synthesis and a high degree of monomer conversion. This innovative two-step polymerization strategy opens up a new opportunity for implementing greener and more environmentally friendly processes for synthesizing biodegradable polyesters.