Immobilizing microalgae in biopolymeric matrices like alginate holds great promise for wastewater treatment. Utilizing alginate beads, we immobilized Scenedesmus sp. microalgae to test its potential in removing paracetamol-contaminated wastewater. By varying alginate and CaCl2 cross-linking agent concentrations, the aim was to identify the most effective combination for optimal performance. Under a 10% calcium chloride solution, alginate beads demonstrated excellent stability. The study delved into the chlorophyll content growth in immobilized microalgae and their ability to eliminate paracetamol from simulated wastewater. Notably, immobilized Scenedesmus sp. showed exceptional performance, achieving 100% removal of 1–2 ppm paracetamol within 24 h. Additionally, chlorophyll content peaked at 3.64 mg/l for a 7 ppm paracetamol concentration, exceeding the control level of 1 mg/l. The investigation into paracetamol removal highlighted an increase in protein from 2.4 mg/l for control to 3.6 mg/l for 7 ppm concentration. At a concentration of 7 ppm, paracetamol exhibited its highest lipid content, approximately 23%. Additionally, the protein and lipid content analysis suggests that immobilized systems may streamline biomass separation from treated wastewater while removing paracetamol from contaminated wastewater.