Functional foods comprise the largest growing food category due to both consumer demands and health claims by manufacturers. Probiotics are considered one of the best choices for meeting these demands. Traditionally, the food vehicle for introducing probiotics to consumers was dairy products, and to expand the benefits of probiotics for a wider range of consumers, the need to use other food items was essential. To achieve this goal while maximising the benefits of probiotics, protection methods used during food processing were tackled. The microencapsulation of probiotics is a promising methodology for achieving this function. This review highlights the use of the microencapsulation of probiotics in order to functionalise food items that initially were not considered suitable for probiotication, such as baked products, or to increase their functionality such as dairy products. The co-microencapsulation of probiotics with other functional ingredients such polyphenol, prebiotics, or omega-3 is also highlighted.