Health-promoting benefits of probiotics after oral administration are challenged by antimicrobial bio-barriers in human gastrointestinal (GI) tract. The objective of this project was to develop an applicable delivery system based on chitosan-coated sub-100 μm Ca2+-alginate gel microcapsules for improved colonic delivery of probiotic lactic acid bacteria (LAB). Flow cytometric analysis (FCM) was utilized to evaluate sucrose and lecithin vesicle on six probiotic LAB strains for the protection against the GI defensive factors - gastric pH and bile acids, respectively. Three subpopulations (intact, injured and dead) could be clearly identified in each sample. In the presence of the protectants, significant expansion of the intact subpopulation was observed, whereas the dead subpopulation was highly decreased. The protectants were then incorporated in Ca2+-alginate microcapsules prepared by an internal-gelation/emulsification technique. With the protection of the reinforced sub-100 μm delivery system, all four examined probiotic strains showed improved survival through an 8-h sequential treatment of the simulated GI fluids. The degradation of the delivery system was also found to respond to the extracted enzymes from human faeces. Approximately 80% of the embedded probiotic bacteria were released within 8-h suspension in the simulated colonic fluid, whereas the release ratio was only 10% in the absence of the colonic enzymes. Additionally, the probiotic delivery system was further confirmed to enhance the storage stability of the probiotic LAB strains and have no obvious adverse influence on the probiotic (e.g. antimicrobial) effect of the embedded probiotic bacteria. The mucoadhesive property of the probiotic delivery system was modified by coating with chitosan. The coated system could retain markedly more probiotic bacteria on HT29-MTX colonic epithelial monolayer. The coatings were further demonstrated in an innovative tensile test to exert stronger mucoadhesion to the colonic mucosa tissues at near neutral pH and with less ambient water, which highly conforms to the physiological environment of the colon. In conclusion, the novel probiotic delivery system was proved to be an efficient vehicle for the colonic delivery of a variety of LAB probiotic strains. The developed probiotic delivery system also indicates the readiness for future research on in vivo confirmation and clinical trials.