This study aims to optimize the biological treatment of wastewater containing tetramethylammonium hydroxide (TMAH), a toxic and poorly biodegradable compound widely used in semiconductor manufacturing. A two-stage pilot-scale treatment system was developed and evaluated. In the first stage, aerobic treatment was applied to convert TMAH into ammonium (NH₄⁺), and the effect of hydraulic retention time (HRT) was examined at 2.0, 2.5, and 3.3 days. The corresponding TMAH conversion rates were 71%, 84%, and 94%, respectively, indicating improved conversion efficiency with longer HRT. In the second stage, the effluent from the aerobic TMAH treatment was mixed with organic wastewater at ratios of 10%, 20%, and 30% and subjected to an anoxic/oxic (A/O) biological treatment. Total nitrogen (T-N) removal efficiencies remained above 87% across all ratios. These findings indicated that most of the toxicity associated with TMAH was alleviated during the aerobic stage, allowing stable nitrogen removal in the second stage. Overall, this study demonstrates that a two-stage biological treatment combining aerobic conversion and A/O processes is effective for treating TMAH-containing nitrogenous wastewater and provides practical guidance for designing and operating treatment systems in the semiconductor industry.