Living organisms are defined by their metabolic activity. Metabolic processes are involved in every aspect of cell function, thereby providing a means of close examination of cellular processes and phenotypes. Deeper knowledge of the metabolic switches and molecular circuitry underlying cell differentiation may enable the monitoring and controlling of cell specification. Our work focuses on the link between metabolism and cell identity. We are using the cell metabolome, the most sensitive and elaborated phenotype, as a readout for shifts in cellular state. We then target the metabolic pathways that are involved in differentiation to regulate developmental and pathological processes. Here will be presented a pronounced metabolic shift at the first hours following exit of pluripotency, implying to the role played by metabolic processes as a driving force for differentiation. The interactions between metabolism, epigenetics and cell identity will be discussed. New insights into possible implications of metabolic regulation of cell fate in early development and in metabolic disease will be highlighted.