Cactus pear (Opuntia ficus-indica) fruit juice is a source of betaxanthin pigments which can be used as a natural yellow food colorant. The HPLC chromatographic pigment pattern corresponding to the betaxanthin-rich extract revealed the presence of four betaxanthins, of which indicaxanthin (proline-betaxanthin) accounts for around 85%. A betaxanthin-rich water-soluble food colorant from cactus pears fruits was produced by spray-drying microencapsulation using maltodextrin as a wall material. The resulting powder was characterized by scanning electron microscopy, and its apparent color was analyzed by spectrometry. The stability of the microcapsules was examined at +20, +4 and -20 °C in the dark during six months of storage. The degradation of betaxanthins was delayed by microencapsulation and their colorant stability increased at lower temperatures. The potential application of the colorant microcapsules was successfully assessed in two food model systems: a yogurt and a soft-drink. Both foods presented an attractive pale yellow color. Pigment retention and color parameters were investigated during storage under controlled conditions. Slight changes in the pigment retention, in both model systems, pointed to excellent preservation in the dark, even after 28 days at 4 °C. However, the presence of light contributed to betaxanthin deterioration. Spray-drying microencapsulation succeeds in reducing volumen of the pigment extract and can be easy in storage and delivery of the powders. It is proved to be a suitable process that can be recommended for stabilizing betaxanthins from cactus pears to be used as water-soluble natural colorants in foods.