The objective of this work was to evaluate the stabilisation of betalains and phenolic compounds extracted from red cactus pear by spray and freeze-drying. After hydroethanolic extraction and partial solvent removal under reduced pressure, the highly coloured extracts were enriched with oca starch and maltodextrin as drying aids in different ratios (100:0, 70:30, and 50:50, oca starch: maltodextrin) prior to spray and freeze-drying. The obtained microencapsulated extract powders were characterised by moisture content, hygroscopicity, solubility and morphology. In addition, the stability of the encapsulated betalains and phenolics was evaluated during storage at room temperature for 105 days. All microcapsules showed high retentions of betacyanins (69.9–86.5% after 105 days), betaxanthins (72.2–81.9%), phenolic compounds (46.5–63.5%) and antioxidant capacity (60.1–64.9%, FRAP method; 49.7–57.5%, ABTS method). The system with 70:30 starch:maltodextrin ratio as drying aids showed the highest values of retention regarding the polyphenol content (63.5%), antioxidant capacity (64.9% to FRAP method) and betacyanin content (86.5%), as well as a low degradation rate constant of betacyanins (1.23 × 10−3 days−1) and a long half-life (563 days). Oca starch used alone or in combination with maltodextrin has been shown to work adequately as a microencapsulating agent and stabilizer of pigments and antioxidants derived from red cactus pear.