An innovative enzymatic polycondensation of dicarboxylic acids and dialcohols in aqueous polymerization media using free and immobilized lipases was developed. Various parameters (type of lipases, temperature, pH, stirring type and rate, and monomer carbon chain length) of the polycondensation in an oil-in-water (o/w) miniemulsion (>80% in water) were evaluated. The best results for polycondensation were achieved with an equimolar monomer concentration (0.5 M) of octanedioic acid and 1,8-octanediol in the miniemulsion and water, both at initial pH 5.0 with immobilized Pseudozyma antarctica lipase B (PBLI). The synthesized poly(octamethylene suberate) (POS) in the miniemulsion is characterized by a molecular weight of 7800 g mol−1 and a conversion of 98% at 45 °C after 48 h of polycondensation in batch operation mode. A comparative study of polycondensation using different operation modes (batch and fed-batch), stirring type, and biocatalyst reutilization in the miniemulsion, water, and an organic solvent (cyclohexane:tetrahydrofuran 5:1 v/v) was performed. Regarding the polymer molecular weight and conversion (%), batch operation mode was more appropriate for the synthesis of POS in the miniemulsion and water, and fed-batch operation mode showed better results for polycondensation in the organic solvent. The miniemulsion and water used as polymerization media showed promising potential for enzymatic polycondensation since they presented no enzyme inhibition for high monomer concentrations and excellent POS synthesis reproducibility. The PBLI biocatalyst presented high reutilization capability over seven cycles (conversion > 90%) and high stability equivalent to 72 h at 60 °C on polycondensation in the miniemulsion and water. The benefits of polycondensation in aqueous media using an o/w miniemulsion or water are the origin of the new concept strategy of the green process with a green product that constitutes the core of the new greener polymer-5B technology.