Betalains are fruit pigments possessing health-giving properties. To isolate the pigments, the juice must be separated from the fruit matrix, which contains biopolymers. The aim of this study was to clarify cactus pear juice by microfiltration to obtain a clarified juice containing betalains. For this purpose, two 0.2 μm pore size microfiltration membranes (ceramic and polymeric) were tested. The permeates were clear, free of turbidity and high in betalains (20%), also containing polyphenols and antioxidant activity, whereas the retained fractions were high in mucilage. The best separation was obtained using the ceramic membrane.