The efficiency of biosorption processes is determined not only by the properties of the biosorbent but also by the operational conditions under which they are applied. This study emphasizes the critical role of operational parameter optimization in enhancing the performance of exhausted coffee husk biochar (ECH-BC) for the removal of Pb (II) and Cu (II) from aqueous solutions. Response surface methodology (RSM) with a Box–Behnken design (BBD) was employed to optimize three key variables: pH, biochar dosage, and contact time. The optimized conditions—pH 6.0, 0.15 g dosage, and 180 minutes for Pb (II), and pH 6.9, 0.05 g dosage, and 135 minutes for Cu(II)—achieved removal efficiencies of 98.1% (32.8 mg/g) for Pb (II) and 96.3% (105.3 mg/g) for Cu (II). Remarkably, these results represent nearly a 100-fold increase in biosorption capacity compared to unoptimized conditions, demonstrating the transformative effect of operational adjustment. Adsorption equilibrium data were better described by the Freundlich isotherm (R² = 0.975 for Pb, R² = 0.885 for Cu), indicating heterogeneous multilayer adsorption with surface complexation as the dominant mechanism. Characterization by SEM-EDX confirmed morphological changes and metal deposition on the biochar surface, while FT-IR spectra revealed the involvement of hydroxyl, carbonyl, and carboxylate functional groups in metal binding. Overall, this study establishes ECH-BC as a cost-effective and sustainable biosorbent, highlighting that optimization of operational parameters is the key factor in unlocking its maximum potential for heavy metal wastewater treatment.