Laccase was successfully hybridized with polyamidoamine (PAMAM) dendrimer-grafted silica-coated hercynite-copper phosphate magnetic hybrid nanoflowers (MHNFs) to increase the catalytic performance of the enzyme and apply in an effective bioremoval of gemifloxacin. For this purpose, the magnetic nanoparticles (MNPs) of hercynite were covered with a silica layer, and the core-shell SiO@hercynite was then modified with PAMAM dendrimer to increase the surface area of the carrier for the enzyme attachment. Subsequently, the whole complex was hybridized with laccase and copper phosphate to attain a large surface area (104.3 m g). The fabricated MHNFs acquired the entrapment yield and efficiency of 90 ± 3% and 66 ± 5%, respectively. The catalytic activity of the fabricated biocatalyst was remained up to 50% after 13 reusability cycles. Approximately 90% of gemifloxacin was removed by the constructed MHNFs after 3 h incubation by adsorption and degradation mechanisms. The biotransformation products were then identified, and degradation pathways were proposed as defluorination, decarboxylation, elimination of a cyclopropyl group, and cleavage of the pyrrolidine moiety. Furthermore, the toxicity of gemifloxacin was effectively diminished against some bacterial strains.