In recent decades, emerging pharmaceutical contaminants, such as personal care items, pharmaceuticals, and disinfectants, have increased alarmingly in aquatic ecosystems. The efficacy of wastewater treatment plants in eliminating these contaminants has been demonstrated. This study aims to find an alternative method, such as using the fluidized bed reactor (FBR) with bacteria to remove amoxicillin from wastewater. The active bacteria Acinetobacter baumannii and Klebsiella pneumoniae were isolated from one of the pharmaceutical factories in Baghdad, Iraq, from Al-Jazeera wastewater, which was used in FBR technology to decompose the antibiotic amoxicillin. The study examined several operational parameters, including pH, total organic carbon (TOC), dissolved carbon dioxide (CO2) concentration, airflow rate, amoxicillin concentration, and bacterial number, while maintaining a constant temperature. High-performance liquid chromatography (HPLC) was used to find the reaction route. The maximum amoxicillin removal efficiency was 93% and 91% for Acinetobacter baumannii and Klebsiella pneumoniae, respectively. For both bacterial species, the pH decreased due to the formation of amino acids and CO2. The suitable operation condition was 5 mg/L of amoxicillin concentration, flow rate of 30 m/s, and the number of bacteria 47 x 105 cfm/mL and 40 x 105 cfm/mL for Acinetobacter baumannii and Klebsiella pneumoniae, respectively. After treatment, the number of bacteria increased due to the degradation of amoxicillin. The steady-state time is found at 64 hours. The organic matter reaction pathway ends at the aromatic amino acid lysine, which kills gram-negative bacteria. This method was found to be successful in removing amoxicillin in low concentrations by using Acinetobacter baumannii. In the future, treating amoxicillin in wastewater using FBR technology with gram-positive bacteria is recommended.