Several health benefits have been associated to probiotics and prebiotics, most of these are involved in the regulation of the host's gut microbiome. Their incorporation to diverse food products has been done to develop potential functional foods. In the case of bakery products, their incorporation has been seen to improve several technological parameters such as volume, specific volume, texture along with sensorial parameters such as flavor and aroma. Scientific literature in this topic has been divided in three main research branches: nutrition, physical quality and sensory analyzes, however, studies rarely cover all of them. Due to the harsh thermal stress during baking, sourdough technology along with microencapsulation of probiotics, has been studied as an alternative to enhance its nutritional values and increase cell viability, though in few occasions. The potential functional baked goods have maintained acceptable physical characteristics and sensorial acceptability, while in some cases an improvement is seen due to the effect of probiotics and prebiotics. The results obtained from several studies done, have shown the viability of developing functional bakery products by applying prebiotics or probiotics. This could be used as an encouragement for more research to be done in this topic.