This study aimed to evaluate the survivability of Lactiplantibacillus plantarum 299v encapsulated in chitosan-coated calcium alginate beads with inulin as prebiotic in simulated gastrointestinal conditions and roselle juice. The concentration of calcium chloride and inulin for L. plantarum 299v microencapsulation was optimised and the survivability of free and microencapsulated L. plantarum was assessed under simulated gastrointestinal conditions. Storage stability of the optimised encapsulated L. plantarum 299v-inulin was determined throughout four (4) weeks of storage in roselle juice at 4 °C and 25 °C. The optimized formula for L. plantarum 299v was 2.0% (w/v) of calcium chloride and 3.0% (w/v) of inulin. Optimized calcium alginate-chitosan L. plantarum 299v microbeads with inulin did not affect (p > 0.05) the bead diameter, with a mean diameter of 685.27 μm, and microencapsulation efficiency of 95%. Encapsulated L. plantarum 299v with inulin showed higher survivability (>107 CFU/mL) than free cells and encapsulated L. plantarum 299v without inulin under simulated gastrointestinal conditions and after four (4) weeks of storage in roselle juice at 4 °C. The results indicate that co-extrusion encapsulation and addition of inulin had improved the viability of L. plantarum 299v in roselle juice by protecting probiotic against unfavourable gastrointestinal conditions and prolonged storage.