Consumers are increasingly interested in a healthy lifestyle, and choosing foods and ingredients with proven human health benefits has become a current trend. Recently, scientific evidence has proven that the use of microorganisms in different food matrices appears to play a key role in the production of bioactive molecules with biological effects on human health. In particular, selected microorganisms with specific traits can be exploited for the production of specific molecules with high nutraceutical value that can be used in the food industry. This review aims to explore the most recent studies that correlate the use of microorganisms to produce high-value molecules through fermentation and synthetic biology, confirming their strategic role in obtaining nutraceuticals for human consumption with health-promoting effects.