Pharmaceutical industry effluents often contain high concentrations of refractory organic solvents, chemical oxygen demand (COD), and total dissolved solids (TDSs). These wastewaters, including N-containing organic solvents known for their persistence and toxicity, pose significant environmental challenges. The study evaluated the efficacy of 3D/Granular Activated Carbon (GAC)/O3 treatment compared to linear process additions when treating real pharmaceutical wastewater, and revealed a 2.73-fold enhancement in COD mineralization. The process primarily involves the direct oxidation of monoprotic organic acids found in real pharmaceutical effluents, such as acetic and formic acid, crucially influencing mineralization rates. Optimal conditions determined via the response surface methodology were 125 g/L GAC, 30 mA/cm2, and 75 mg/L O3, achieving high total organic carbon (TOC) and COD removal efficiencies of 87.19 ± 0.19% and 89.67 ± 0.32%, respectively (R2 > 0.9), during verification runs. Current density emerged as the key parameter for organic abatement, aligning with the emphasis on direct oxidation at the anode surface. This integrated approach enhances biodegradability (BOD5/COD) and reduces acute toxicity associated with persistent N-containing solvents, demonstrating promising applications in pharmaceutical wastewater treatment.