Resveratrol, carnosic acid and hernandulcin are considered as nutraceuticals with potential application against pandemic health problems such as obesity, type 2 diabetes mellitus and diverse types of cancer. Basic and applied studies centered on metabolic engineering have emerged to scale the production of these molecules. The natural production of resveratrol by filamentous fungi represents a novel source for the obtainment of new coding sequences usable for metabolic engineering approaches. On the other hand, first attempts to get the controlled synthesis of carnosic acid have been achieved through engineered yeasts whereas the final biosynthetic step of hernandulcin biosynthesis remains unresolved. Despite the current status of hernandulcin biosynthesis, interesting attempts have been done in order to scale its production. Herein, we discuss the most recent advances in the controlled synthesis of these nutraceuticals.