Environmental water sources are under increasing threat due to the addition of harmful chemicals that are not addressed by conventional water treatment processes. To work on this concern, the current study aimed to synthesize sono-assisted Fe-modified activated carbon–chitosan (FeAcC) composite and construct a laboratory-scale ozone-integrated fluidized bed reactor (FBR) to eliminate phenolphthalein (php). After 120 min of incubation, the adsorbent demonstrated a 27.28 mg g−1 of php adsorption capacity at a pH of 4 with 0.5 g L−1 of adsorbent dosage. The adsorption efficacy and mechanism were defined using isotherm and kinetic models. The study investigated the impact of different factors, including initial concentration, reuse of FeAcC, recirculation flow rate, and hydraulic retention time (HRT), on the efficiency of php removal. The optimum removal efficiency was observed at approximately 95% after 20 min of operation at 1.5 L min−1 recirculation flow rate (batch FBR) and 70 min of HRT (continuous FBR) under a 400 mg h−1 ozonation rate. Experimental parameters were optimized using response surface methodology with central composite design to improve php removal. The large-scale implementation of the findings in the future can be a step for adding new technology for clean water treatment processes for emerging toxic organic pollutants.