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Bioactive compounds are sensitive to many factors, and they can alter the sensory characteristics of foods. Microencapsulation could be a tool to provide protection and allow the addition of bioactives in new matrices, such as sugarcane juice. This study focused on producing and evaluating the potential function of probiotics and proanthocyanidin-rich cinnamon extract (PRCE), both in free and encapsulated forms when added to sugarcane juice. The pure sugarcane juice treatment T1 was compared with other sugarcane juices to which bioactive compounds had been added; T2, a non-encapsulated Bifidobacterium animalis subsp. lactis (BLC1); T3, a non-encapsulated BLC1 and PRCE; T4, BLC1 microcapsules; and T5, with BLC1 and PRCE microcapsules. The samples were morphologically, physicochemically, rheologically, and sensorially characterized. Samples were also evaluated regarding the viability of BLC1 during the juice's storage at 4 °C. It was possible to produce probiotic sugarcane juice with non-encapsulated BLC1, but not with the addition of free PRCE, which in its free form reduced the viability of this microorganism to < 1 log CFU/mL after 7 days. The microcapsules were effective to protect BLC1 during juice storage and to maintain high contents of phenolic and proanthocyanidin compounds, although the products containing these had their viscosity altered and were less accepted than either the control or those with non-encapsulated BLC1.