To combat the rise in caloric overconsumption, new ways of satisfying sweet desires must reduce caloric intake without sacrificing palatability. Rare sugars and steviol glycosides are emerging classes of naturally occurring alternative sweeteners. They have gained interest for industrial production due to their low-calorie content, desirable flavor, and notable bioactivity for potential broader applications. Microbial production offers unique benefits to efficiently produce rare sugars and steviol glycosides. Particularly, the model organism Escherichia coli is capable of irreversible rare sugar production using phosphorylation–dephosphorylation chemistry using its native components. Saccharyomyces cerevisiae, another model organism, has emerged as an alternative production platform for producing various steviol glycosides. Herein, we summarize the chemical and enzymatic production pathways that establish microbial sweetener production.