This study investigated the electro-mineralization of chloroquine (CQ) in a filter-press-type flow reactor using two BDD electrodes operating in batch recirculation mode. The optimal operating parameters were established using response surface methodology (RSM) and central composite rotatable design (CCRD) with three parameters: current density (j), initial pH (pH₀), and volumetric flow rate (Q), with the mineralization efficiency of (CQ) and specific energy consumption (SEC) as responses. Optimal operating parameters were j = 155.0 mA/cm², pH₀ = 9.75, and Q = 0.84 L/min within a reaction time of 9 h, leading to a maximum mineralization efficiency of CQ of 52.59% and a specific energy consumption of 15.73 kW/mg TOC, with a total operating cost of USD 0.18 per liter. Additionally, an ultra-high-performance chromatography study identified three by-products (4-amino-7-choloroquinoline, formic acid, and acid acetic) of CQ degradation. Furthermore, the phytotoxicity test indicates that the electrochemical wastewater proposed decreased the effluent’s phytotoxicity, and an increase in the percentage of Vigna radiata germination was observed. The carbon footprint of optimized electrochemical mineralization of chloroquine is 2.48 kg CO₂ eq., representing a 48% reduction in cumulative energy demand (CED) when the source of energy is a mixture of fossil fuels (50%), wind (25%), and photovoltaic (25%) energy.