The presence of micropollutants in wastewater is one of the most significant environmental challenges. Particularly, pollutants such as pharmaceutical residues present high stability and resistance to conventional physicochemical and biological degradation processes. Thus, we aimed at immobilizing a laccase enzyme by two different methods: the first one was based on producing alginate-laccase microcapsules through a droplet-based microfluidic system; the second one was based on covalent binding of the laccase molecules on aluminum oxide (Al2O3) pellets. Immobilization efficiencies approached 92.18% and 98.22%, respectively. Laccase immobilized by the two different methods were packed into continuous flow microreactors to evaluate the degradation efficiency of acetaminophen present in artificial wastewater. After cyclic operation, enzyme losses were found to be up to 75 µg/mL and 66 µg/mL per operation cycle, with a maximum acetaminophen removal of 72% and 15% and a retention time of 30 min, for the laccase-alginate microcapsules and laccase-Al2O3 pellets, respectively. The superior catalytic performance of laccase-alginate microcapsules was attributed to their higher porosity, which enhances retention and, consequently, increased the chances for more substrate–enzyme interactions. Finally, phytotoxicity of the treated water was lower than that of the untreated wastewater, especially when using laccase immobilized in alginate microcapsules. Future work will be dedicated to elucidating the routes for scaling-up and optimizing the process to assure profitability.