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In the present investigation, an ecofriendly magnetic inorganic-protein hybrid system-based enzyme immobilization was developed using partially purified laccase from <i>Trametes versicolor</i> (<i>Tv</i>Lac), Fe₃O₄ nanoparticles, and manganese (Mn), and was successfully applied for synthetic dye decolorization in the presence of enzyme inhibitors. After the partial purification of crude <i>Tv</i>Lac, the specific enzyme activity reached 212 U∙mg total protein⁻¹. The synthesized Fe₃O₄/Mn₃(PO₄)₂-laccase (Fe₃O₄/Mn-<i>Tv</i>Lac) and Mn₃(PO₄)₂-laccase (Mn-<i>Tv</i>Lac) nanoflowers (NFs) exhibited encapsulation yields of 85.5% and 90.3%, respectively, with relative activities of 245% and 260%, respectively, compared with those of free <i>Tv</i>Lac. One-pot synthesized Fe₃O₄/Mn-<i>Tv</i>Lac exhibited significant improvements in catalytic properties and stability compared to those of the free enzyme. Fe₃O₄/Mn-<i>Tv</i>Lac retained a significantly higher residual activity of 96.8% over that of Mn-<i>Tv</i>Lac (47.1%) after 10 reuse cycles. The NFs showed potential for the efficient decolorization of synthetic dyes in the presence of enzyme inhibitors. For up to five reuse cycles, Fe₃O₄/Mn-<i>Tv</i>Lac retained a decolorization potential of 81.1% and 86.3% for Coomassie Brilliant Blue R-250 and xylene cyanol, respectively. The synthesized Fe₃O₄/Mn-<i>Tv</i>Lac showed a lower acute toxicity towards <i>Vibrio fischeri</i> than pure Fe₃O₄ nanoparticles did. This is the first report of the one-pot synthesis of biofriendly magnetic protein-inorganic hybrids using partially purified <i>Tv</i>Lac and Mn.