In this work, five different magnetic biofilters, containing magnetic nanoparticles (142 nm), immobilized laccase on nanoparticles (190 nm) and permanent magnetic elements, such as neodymium magnets and metallic meshes, were designed, manufactured and tested. The five types of filters were compared by measuring the decolorization of Congo Red dye inside bioreactors, the half-life of the filters and the amount of magnetic nanoparticle and enzyme lost during multiple cycles of operation. Filters containing laccase immobilized on magnetite (Laccase-magnetite), permanent magnets and metallic mesh presented the highest Congo Red decolorization (27%) and the largest half-life among all types of filters (seven cycles). The overall dye decolorization efficiencies were 5%, 13%, 17%, 23%, and 27% for the paper filter, paper filter with magnetite, paper filter with Laccase-magnetite, paper filter with Laccase-magnetite with magnets and paper filter with Laccase-magnetite with magnets and metallic mesh, respectively. Although the highest losses of magnetite occurred when using the filters containing magnets (57 mg), the use of permanent magnetic elements in the filters increased the half-life of the filter three-fold compared to the filters without enzymatic properties and two-fold compared to the filters with Laccase-magnetite. Results indicate that the novel use of permanent magnetic elements improved the nanoparticle retention in the filters and promoted the mass transfer between the dye and the biocatalyst to enhance wastewater treatment.