Bread is one of the most widely embraced food products and is highly accepted by consumers. Despite being rich in complex carbohydrates (i.e., starch), bread is generally poor in other micro- and macronutrients. Rising consumer demand for healthier food has resulted in the growth of studies focused on bread fortification with bioactive ingredients (i.e., vitamins, prebiotics, and vegetable extracts). However, the baking process leads to the reduction (or even lessening) of the added substance. In addition, the direct inclusion of bioactive compounds and additives in bread has other limitations, such as adverse effects on sensory characteristics and undesirable interaction with other food ingredients. Encapsulation allows for overcoming these drawbacks and at the same time improves the overall quality and shelf-life of bread by controlling the release, protection, and uniform distribution of these compounds. In the last ten years, several studies have shown that including micro/nano-encapsulated bioactive substances instead of free compounds allows for the enrichment or fortification of bread, which can be achieved without negatively impacting its physicochemical and textural properties. This review aims to identify and highlight useful applications in the production of new functional bread through encapsulation technology, summarizing the heath benefit and the effect of microcapsule inclusion in dough and bread from a technological and sensory point of view.