The wastewater generated from citric acid production has a high organic loading content. The treatment and reuse of citric acid wastewater with high organic loading become extremely important. In this study, the performance of calcium hydroxide (Ca(OH)2) precipitation as a low-cost and environmentally friendly pre-treatment method and aerobic membrane bioreactor (MBR) combined treatment system was investigated for the treatment of citric acid (CA) wastewater. At the first step, optimization parameters such as agitation speed (100, 150, 200 rpm), temperature (30, 50, 70 °C), and reaction time (2, 4, 6 h) for Ca(OH)2 precipitation as a pre-treatment method were investigated using response surface methodology (RSM) to achieve maximum chemical oxygen demand (COD) removal. Experimental sets were designed using Box-Behnken Design. As a result of pre-treatment with Ca(OH)2 precipitation, a COD removal efficiency of 97.3% was obtained. Then, pre-treated CA wastewater was fed continuously to the MBR process for 10 days, which was the second stage of the combined process. As a result of the MBR process, 92.0% COD removal efficiency was obtained for 24 h HRT and 10 days SRT. In total, 99.8% COD removal efficiency was obtained when combined process was used and COD concentration decreased from 52,000–114 mg/L. For the treatment and reuse of wastewater from citric acid production, Ca(OH)2 precipitation and MBR combined treatment systems demonstrated an effective strategy.