Intracellular metabolites play a crucial role in characterizing and regulating corresponding cellular activities. Tracking intracellular metabolites in real time by traditional means was difficult until the powerful toolkit of genetically encoded biosensors was developed. Over the past few decades, iterative improvements of these biosensors have been made, resulting in the effective monitoring of metabolites. In this review, we introduce and discuss the recent advances in the use of genetically encoded biosensors for tracking some key metabolites, such as ATP, cAMP, cGMP, NADH, reactive oxygen species, sugar, carbon monoxide, and nitric oxide. A brief phylogeny of fluorescent proteins and several typical construction modes for genetically encoded biosensors are also described. We also discuss the development of novel RNA-based sensors, which are genetically encoded biosensors active at the transcriptional level.