Complete characterization of microfiltered red-purple pitaya colorant (MRPPC) and its potential applications in foods is described. Using sensorial analysis, products that use carmine or beetroot dye as a food colorant in their formulations were compared. The effect of storage under refrigeration on the microbiological, physicochemical, and chemical changes of MRPPC were evaluated. The results showed that UPLC-ESI-QTOF-MSE was effective for the simultaneous determination of twenty metabolites, putatively identified as carbohydrates, flavonoids, and betalains. The MRPPC was shown to have microbiological and physicochemical stability through twelve weeks of storage, and chemometric analyses efficiently distinguished the metabolic profile in each storage period. Sensory analysis revealed that the MRPPC was useful as a food colorant in yogurt, where it improved color quality without affecting aroma and other characteristics. These results indicate that MRPPC is promising food ingredient as a natural red-purple colorant.