In this study, a multistage treatment system was proposed to treat real pharmaceutical wastewater containing the antibiotic amoxicillin. Ozonation (O3), and ozonation combined with aerobic biodegradation, were performed. The real pharmaceutical wastewater presented a high concentration of organic matter (TOC: 803 mg C·L−1 and COD: 2775 mg O2·L−1), significant amoxicillin content (50 mg L−1) and acute ecotoxicity (Aliivibrio fischeri aTU: 48.22). Ozonation proved to be effective for amoxicillin degradation (up to 99%) and the results also indicated the removal of the original colour of the wastewater, with average consumption of 1 g of ozone. However, the ozonation system alone could not achieve complete mineralization. Therefore, a combination of ozonation and biodegradation in a multistage system was proposed in order to improve cost and treatment efficiency. The multistage treatment system presented promising results, achieving degradation of more than 99% of the amoxicillin, more than 98% of the original chemical oxygen demand (COD), and 90% of initial toxicity, with the consumption of approximately 500 mg of ozone. This indicates that this system could prevent dangerous and biorecalcitrant antibiotics from entering water resources. Display omitted •Multistage system (aerobic biological + O3) to treat real pharmaceutical effluent.•The combined treatment was able to remove >99% of the original amoxicillin content.•More than 98% of the original COD and the original colour were abated.•Moreover, more than 90% of Aliivibrio fischeri original acute toxicity was removed.