The optimization for poly-β-hydroxyalkanoate production was carried out with nutrient removal efficiency for total organic carbon (TOC), phosphate, and nitrate from palm oil mill effluent waste. The experiment was conducted in a fabricated fed-batch reactor and the data obtained was analyzed using central composite rotatable design and factorial design for response surface methodology as a systematic approach for designing the experiment statistically to obtain valid results with minimum effort, time, and resources. The analysis of numerical optimization with propagation of error showed that 66 % of poly-β-hydroxyalkanoate production can be obtained with nutrient removal of TOC and nitrate by 19 and 3 %, respectively. However, phosphate removal efficiency was not found to be much effective. More over, the chemical oxygen demand: nitrogen phosphate (509 g/g N), chemical oxygen demand: phosphate (200 g/g P), air flow rate (0.59 L/min), substrate feeding rate (20 mL/min), and cycle length (20 h) were the optimized variables for maximum poly-β-hydroxyalkanoate production and nutrient removal.