In the quest for eco-conscious innovations, this research was designed for the sustainable synthesis of magnetite (Fe3O4) nanoparticles, using ferric chloride hexahydrate salt as a precursor and extract of Eucalyptus globulus leaves as both a reducing and capping agent, which are innovatively applied as a photocatalyst for the photocatalytic degradation of antibiotics “ciprofloxacin and amoxicillin”. Sugar cane bagasse biomass, sugar cane bagasse pyrolyzed biochar, and magnetite/sugar cane bagasse biochar nanocomposite were also synthesized via environmentally friendly organized approaches. The optimum conditions for the degradation of ciprofloxacin and amoxicillin were found to be pH 6 for ciprofloxacin and 5 for amoxicillin, dosage of the photocatalyst (0.12 g), concentration (100 mg/L), and irradiation time (240 min). The maximum efficiencies of percentage degradation for ciprofloxacin and amoxicillin were found to be (73.51%) > (63.73%) > (54.57%) and (74.07%) > (61.55%) > (50.66%) for magnetic nanocomposites, biochar, and magnetic nanoparticles, respectively. All catalysts demonstrated favorable performance; however, the “magnetite/SCB biochar” nanocomposite exhibited the most promising results among the various catalysts employed in the photocatalytic degradation of antibiotics. Kinetic studies for the degradation of antibiotics were also performed, and notably, the pseudo-first-order chemical reaction showed the best results for the degradation of antibiotics. Through a comprehensive and comparative analysis of three unique photocatalysts, this research identified optimal conditions for efficient treatment of drug-contaminated wastewater, thus amplifying the practical significance of the findings. The recycling of magnetic nanoparticles through magnetic separation, coupled with their functional modification for integration into composite materials, holds significant application potential in the degradation of antibiotics.