The delivery of probiotics to different sites of action within the human body might help to prevent and treat several diseases. Here, we describe a microcapsule-based system for delivery of probiotic bacteria, as vegetative cells or spores, which promotes their prolonged survival and efficient revival, and successful colonisation of the target surface. This system is proposed for local delivery into periodontal pockets. Encapsulation of the probiotic bacteria was based on alginate crosslinking with calcium ions. This was performed by prilling the polymer dispersion supplemented with the probiotic using membrane vibration technology, followed by chitosan coating by polyelectrolyte complexation. The microcapsules were 120–150 μm in diameter, and were dried by lyophilisation. The chitosan coating increased the specific surface area and improved the bioadhesion potential, with no negative impact on viability and growth kinetics of the probiotic bacteria. Chitosan represents a barrier, which promotes sustained release of the probiotic bacteria. Vegetative bacteria were encapsulated at 2 × 108 CFU/g dry microcapsules, which represented ˜5% of the prepared microcapsules, with stable viability for at least 2 months. Encapsulation of bacterial spores was greater, at 2 × 1010 CFU/g dry microcapsules, achieving 100% of microcapsules with incorporated revivable spores.