Stevia sugar is widely used in food owing to its advantages of low calorie content and high sweetness. In the production of stevia sugar, stevia leaves are immersed in water to obtain a crude liquor, which contains many impurities, such as proteins, polysaccharides, organic acids, etc. These impurities are removed typically by coagulation and filtration. At present, suppliers of stevia mainly use a “lime + ferrous sulfate (FeSO4)” process as the pretreatment, but residual SO42− can cause hydrogen sulfide corrosion and Ca2+ can affect the safety of subsequent boilers in the process. In this study, polyaluminium ferric chloride (PAFC) was evaluated as a superior coagulant to FeSO4, together with ultrafiltration (UF) and nanofiltration to remove flocs and other organic contaminants. It was found that coagulation by PAFC out-performed FeSO4 and was unaffected by pH, while the performance of FeSO4 was sensitive to pH. At pH 10, FeSO4 had an enhanced coagulation efficiency, but formed soluble Fe2+ complexes with organic substances in the original solution, which adversely affected the quality of the filtrate. Compared with a UF membrane, the NF membrane was more effective in removing contaminants, and more tolerant to membrane fouling. In addition to hydrodynamic flux, measurement of trans-membrane electrical current were used to reflect the severity of membrane fouling. The combination of PAFC as coagulant without pH adjustment, and ultrafiltration, was found to be a simpler and superior treatment for stevia liquor with a high degree of contaminant separation, and avoidance of problems caused by SO42− and Ca2+.