Phenolic compound extracts from Hibiscus sabdariffa L. (HS) exhibit promising functional and technological properties; however, their application in foods is limited by their susceptibility to degradation, making microencapsulation a promising strategy. This study aimed to test different extraction conditions for phenolic compounds from HS, microencapsulate the HS extract, incorporate the selected microcapsules into a fermented dairy beverage based on buttermilk (a dairy co-product) containing Lactobacillus gasseri (L. gasseri), and evaluate stability during 28 days of refrigerated storage. The use of 70% cereal alcohol resulted in the highest recovery of bioactive compounds and antioxidant capacity. The microcapsules exhibited an acidic pH, solubility exceeding 75%, encapsulation efficiency ranging from 48.86% to 92.12%, and heterogeneous morphology across samples. The beverage demonstrated satisfactory physicochemical stability and slow degradation of phenolic compounds (half-life [t½] of 34.5 days). Finally, ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) confirmed the presence of 14 compounds in the HS calyces, microcapsules, and beverage, indicating the retention of these compounds through to the final product. Overall, microencapsulation enabled the incorporation of bioactive HS compounds into a fermented dairy matrix, confirming their potential as a functional ingredient and natural colorant.