A new strategy for the preparation of biocatalysts based on enzyme immobilization was explored, leading to cross-linked enzyme aggregate onto magnetic particles (CLEMPA). Lipase enzyme from Aspergillus niger was precipitated from aqueous solution followed by cross-linking of the enzyme aggregates onto magnetic particles using glutaraldehyde as cross-linker. An optimization study has been carried out for the CLEMPA approach to determine the best experimental conditions for both preparation steps (i.e. enzyme precipitation and cross-linking of the enzyme aggregates onto magnetic particles). Type and concentration of the precipitation agent, type and size of magnetic particles, ratio of lipase to magnetic particles, concentration of the cross-linker and growth time of CLEMPA clusters were the experimental factors taken under investigation. Characterization of CLEMPA biocatalyst considering the cluster size and lipase loading was performed using light scattering detection and UV-vis spectrophotometric techniques. The catalytic capacity of CLEMPA biocatalyst was tested with the “green” alternative of glycerol carbonate (GlyC) synthesis. CLEMPA catalyzed the conversion of glycerol to GlyC with an excess of dimethyl carbonate (DMC) providing solvent-free conditions for the reaction. These experiments resulted in encouraging biocatalytic performance with 61% glycerol conversion, 55% GlyC yield and 90% selectivity in GlyC. CLEMPA biocatalyst was also tested in the reaction of “crude” glycerol extracted from the biodiesel process, with similar performance results. Recycling experiments for 20 successive reaction cycles demonstrated the robustness of the prepared CLEMPA structure.