In this work, the design, manufacture, and testing of three different magnetic microreactors based on torus geometries (i.e., one-loop, two-horizontal-loop, and two-vertical-loop) is explored to increase the enzyme-based transformation of dyes by laccase bio-nanocomposites, improve the particle suspension, and promote the interaction of reagents. The laccase enzyme was covalently immobilized on amino-terminated silanized magnetite nanoparticles (laccase-magnetite). The optimal configuration for the torus microreactor and the applied magnetic field was evaluated in silico with the aid of the CFD and particle tracing modules of Comsol Multiphysics®. Eriochrome Black T (EBt) dye was tested as a biotransformation model at three different concentrations, i.e., 5 mg/L, 10 mg/L, and 20 mg/L. Phenol oxidation/removal was evaluated on artificial wastewater and real wastewater. The optimal catalytic performance of the bionanocomposite was achieved in the range of pH 4 to 4.5. A parabolic movement on the particles along the microchannels was induced by the magnetic field, which led to breaking the stability of the laminar flow and improving the mixing processes. Based on the simulation and experiments conducted with the three geometries, the two-vertical-loop microreactor demonstrated a better performance mainly due to larger dead zones and a longer residence time. Additionally, the overall dye removal efficiencies for this microreactor and the laccase-magnetite bionanocomposite were 98.05%, 93.87%, and 92.74% for the three evaluated concentrations. The maximum phenol oxidation with the laccase-magnetite treatment at low concentration for the artificial wastewater was 79.89%, while its phenol removal efficiency for a large volume of real wastewater was 17.86%. Treatments with real wastewater were carried out with a larger volume, equivalent to 200 biotransformation (oxidation) operating cycles of those carried out with dyes or phenol. Taken together, our results indicate that the novel microreactors introduced here have the potential to process wastewaters rich in contaminant dyes in continuous mode with efficiencies that are attractive for a potential large-scale operation. In this regard, future work will focus on finding the requirements for scaling-up the processes and evaluating the involved environmental impact indexes, economic performance, and different device geometries and processing schemes.