A unique double-layered vehicle was fabricated for the first time based on a millifluidic/direct gelation to encapsulate probiotics. Free probiotic bacteria are usually very sensitive to severe gastrointestinal conditions and maintaining their survival when passing through the digestive tract is essential. The effects of alginate concentration (20–30 g/L), flow rates of alginate (0.8–1.2 mL/min), and W/O emulsion (0.5–0.7 mL/min) on encapsulation efficiency (EE), size, and sphericity of core–shell millicapsules were optimized for encapsulation of Bifidobacterium animalis subsp. lactis and Lactobacillus plantarum. The optimized calcium-alginate millicapsule was spherical (0.97 ± 0.01 SF), with an average diameter of 4.49 ± 0.19 mm, and encapsulation efficiency of 98.17 ± 0.5 %. Two strains were encapsulated separately in W/O emulsion as a core of the millicapsule. After coating with chitosan, the encapsulation yield of the bacteria, survival rates under simulated gastrointestinal (GI) conditions, and viability during storage were determined. Survival efficiency of B. animalis subsp. lactis and L. plantarum after millifluidic encapsulation were found to be 92.33 and 90.81 %, respectively. Cell viability of encapsulated probiotics after passing through the GI system was improved (7.5 log CFU mL−1 for both strains). Although the viability of the encapsulated probiotics stored at −18 °C for five months significantly decreased (p<0.05), the number of live cells was approximately in accordance with the standard definition of long-term probiotic survival (6 log CFU/g). This work provides a pathway for the construction of an innovative delivery system with high efficiency and protective effects for probiotics.