A recombinant lipase B from Candida antarctica (LipB) in Pichia pastoris was synthesized through submerged fermentation using crude glycerin as substrate. The immobilization of this enzyme on the core–shell polymeric supports is an effective alternative for its application. The supports with distinct levels of hydrophobicity were produced through combined suspension and emulsion polymerization in pilot scale. Particles with distinct compositions were synthesized (PMMA/PMMA; PMMA‐co‐DVB/PMMA‐co‐DVB; and PS‐co‐DVB/PS‐co‐DVB) and employed on the immobilization of the produced lipase (LipB) and the commercial enzyme (CalB). The morphological properties (specific area, average pore diameter, specific volume of pores, and hydrophobicity level) and the influence of the polymerization conditions on the morphology of the supports were studied. The thermal stability of such biocatalysts was also investigated in the presence of calcium cation (Ca⁺²), maintained 100% of the activity after 3 h at 50°C when the PMMA‐co‐DVB/PMMA‐co‐DVB was employed. The synthesized enzyme and supports manufactured in pilot scale were employed successfully for production of esters using residual fatty acids as substrates, adding value to these raw materials and increasing the ranges of possible applications.