The occurrence of micropollutants in aqueous matrices has become a global concern and a challenge for wastewater treatment plants. Monitoring their toxicity has shown that these compounds, even at low concentrations, pose risks to human and environmental health. Therefore, our study aimed to prospect immobilization strategies for non-commercial oxidoreductase enzymes and insert them in the context of pollutant remediation. The enzymatic extract was obtained by submerged fermentation of the fungus Trichoderma koningiopsis in an alternative substrate, consisting of fresh microalgal biomass from the phycoremediation process. The immobilization efficiency of peroxidase (POD) was evaluated by monitoring the residual activity (RA) and the discoloration potential (DP) of a synthetic dye solution. Concomitantly, the catalytic properties of free POD were explored, and the most promising storage strategy to maintain the enzymatic activity was studied. Guaiacol peroxidase from T. koningiopsis expressed specific activity of up to 7801.1 U mg− 1 in the free form, showing stability when subjected to up 80°C in a pH range between 4.0–8.0. Furthermore, the bioproduct immobilized on magnetic nanoparticles expressed up to 688% RA and 100% DP. An increase in the RA of the enzyme, both in free and immobilized form, was also observe after storage for up to 8 months. The synthesized magnetic nanozymes showed good reusability, maintaining 13546.4 U mg− 1 after ten cycles and removing 93% of color in a second batch. Toxicological evaluation with Allium cepa indicated that the enzymatic process of color removal with immobilized POD, despite maintaining unwanted cytotoxic effects, was essential to eliminate genotoxic effects. In this sense, the immobilization processes of T. koningiopsis peroxidase presented in our work are promising for the enzyme market and for the wastewater treatment sector.