The delivery of beneficial bacteria to the gut microbiome holds a promise to avert and treat diseases such as ariboflavinosis. Nevertheless, adverse gastrointestinal (GI) conditions, a high concentration of reactive oxygen species (ROS), exhausted mucus layer, constant peristalsis of the gastrointestinal tract, and complex pathological microenvironment result in low oral bioavailability lead to limited intestinal colonization of probiotics and affect their related health benefits. Herein, we established a bio-based strategy of double-layer gelatin-mucin-alginate and chitosan-mucin-alginate microcapsules that endow the transplanted riboflavin (vitamin B2) over-producing strain Lactobacillus plantarum B2 with robust resistance to adverse environments and remarkable adhesiveness to the intestine. The outer gelatin (or chitosan) membrane was observed by building a gelatin-genipin (or chitosan-genipin) fluorescent complex. We demonstrated that co-encapsulating with mucin and the secondary coating of gelatin or chitosan could effectively maintain the regular surface morphology of gel beads and protect probiotics during the lyophilization process, possibly by improving the internal cross-linking and mechanical strength of the microcapsules. The encapsulated probiotic strain was endowed with strong resistance during storage, simulated gastrointestinal digestion fluid, and ROS exposure. In addition, co-embedded mucin augmented the adherence rate of L. P. B2 on the simulated intestinal mucus. Most importantly, microcapsule encapsulation not only retained the probiotic potential of L. P. B2 but also improved the B2 production during soymilk fermentation. Altogether, the encapsulation strategy can be used as an effective way to deliver explicit probiotics to the gut microbiota for the intestinal colonization of probiotics to deliver B2 in the human gut.