The coconut desiccant industry produces wastewater with high concentrations of suspended solids and turbidity, resulting in negative impacts to the environment if discharged without adequate treatment. The wastewater produced requires appropriate flocculant and coagulant compounds for treatment via the clarification process. Commercial coagulants raise many environmental concerns pertaining to the release of toxic metal residues and traces of chloride and sulphate ions in the treated water. The use of eco-friendly coagulants as an alternative for commercial coagulants in wastewater treatment is on the rise. Several factors that influence clarification performance during treatment includes coagulant dosage, flocculant dosage, and mixing rate of coagulation–flocculation process. The aim of this research is to analyze the effectiveness of using a natural coagulant, Moringa oleifera extract in the removal of suspended solids and turbidity from the coconut desiccant industry wastewater. The Response Surface Methodology approach was used to optimize the concentration of coagulant and flocculant dosed along with mixing rate. The results were measured as maximum percentage removal of suspended solids and turbidity. Coconut desiccant wastewater was collected over a period of five days. Moringa extract was produced via dilution of fat free Moringa seed powder with salt solution at a fixed ratio. The percentage removal of both suspended solids and turbidity was in the range of 85.4–95.1% and 85.2 to 94.8% respectively, based on multiple jar tests conducted. The model generated for optimization is a quadratic model. The optimization produced an optimum point of treatment, which is 12.00 mg/L of Moringa extract as coagulant, 12.660 ml/L of anionic polymer as flocculant and a mixing rate of 90 revolutions per minute, resulting in 93.997% and 93.735% removal of suspended solids and turbidity, respectively, proving a successful treatment of coconut desiccant wastewater.