Pulp (CP) and ultrafiltered (UF) cactus pear extracts were encapsulated with Capsul (C) by applying a central composite design (CP-C and UF-C systems) by spray-drying. To evaluate the effect of the extract, microparticles obtained under optimal conditions were characterised and stored at 60 C. Betacyanin and betaxanthin encapsulation efficiency reached values above 98% for both systems studied. This efficiency was attributed to strong interactions between betalains and the polymer. Betalain degradation in CP-C and UF-C microparticles followed pseudo-first order kinetics. The betacyanin degradation rate constant was significantly higher for CP-C than for UF-C. These results suggested that the mucilage or higher sugar content of CP increased the hygroscopicity of the CP-C microparticles, leading to the degradation of betalain. The hydrolysis pathway was the main mechanism of betanin degradation during microparticle storage. These results demonstrate the potential utility of both CP-C and UF-C microparticles as natural colourants for healthy foods.