Conventional wastewater treatment processes are often unable to remove antibiotics with resistant compounds and low biological degradation. The need for advanced and sustainable technologies to remove antibiotics from water sources seems essential. In this regard, the effectiveness of a spinning disc photocatalytic reactor (SDPR) equipped with a visible light-activated Fe3O4@SiO2-NH2@CuO/ZnO core–shell (FSNCZ CS) thin film photocatalyst was investigated for the decomposition of amoxicillin (AMX), a representative antibiotic. Various characterization techniques, such as TEM, FESEM, EDX, AFM, XRD, and UV–Vis-DRS, were employed to study the surface morphology, optoelectronic properties, and nanostructure of the FSNCZ CS. Key operating parameters such as irradiation time, pH, initial AMX concentration, rotational speed, and solution flow rate were fine-tuned for optimization. The results indicated that the highest AMX decomposition (98.7%) was attained under optimal conditions of 60 min of irradiation time, a rotational speed of 350 rpm, a solution flow rate of 0.9 L/min, pH of 5, and an initial AMX concentration of 20 mg/L. Moreover, during the 60 min irradiation time, more than 69.95% of chemical oxygen demand and 61.2% of total organic carbon were removed. After the photocatalytic decomposition of AMX, there is a substantial increase in the average oxidation state and carbon oxidation state in SDPR from 1.33 to 1.94 and 3.2, respectively. Active species tests confirmed that ·OH and ·O2− played a dominant role in AMX decomposition. The developed SDPR, which incorporates a reusable and robust FSNCZ CS photocatalyst, demonstrates promising potential for the decomposition of organic compounds.