In this study, co-encapsulation technique was used to produce microcapsules utilized as a multi-functional delivery vehicle for valuable nutritional compounds. These compounds including probiotic bacteria namely Bifidobacterium lactis BB12, fish oil and pomegranate peel extract (PPE) that is rich in polyphenols as revealed by HPLC analysis. Microcapsules with different formulae were produced and the encapsulation efficiency (EE) of probiotic bacteria and fish oil was evaluated. Results suggest that the presence of fish oil and PPE enhanced the EE of probiotic bacteria and this positive effect increased with the increasing of the mentioned 2 components. Moreover, PPE protected the encapsulated probiotic bacteria from declining during the storage for 30 days. PPE acted as an effective antioxidant and decreased the formation of both dienes and trienes and assisted in the preservation of the unsaturated moiety of fish oil compared to other microcapsules with no PPE. As food application, the multi-functional microcapsules were incorporated into soft cheese. Oxidative analysis of fish oil was carried out during cheese storage and showed similar results to those found with free microcapsules. In addition, the presence of probiotic bacteria and/or PPE in microcapsules decreased the deterioration and delayed the oxidation of fish oil. On the other hand, probiotic survivability showed to be similar in different microcapsules incorporated into cheese.