Significance Glycerol-3-phosphate (Gro3P) lies at the crossroads of glucose, lipid, and energy metabolism in mammalian cells and is thought to participate in glycolysis or in gluconeogenesis, lipid synthesis, and Gro3P electron transfer shuttle to mitochondria. We now report a previously unidentified pathway of Gro3P metabolism in mammalian cells with the identification of Gro3P phosphatase (G3PP) that can directly hydrolyze Gro3P to glycerol. We observed that G3PP expression level controls glycolysis, lipogenesis, lipolysis, fatty acid oxidation, cellular redox, and mitochondrial energy metabolism in β-cells and hepatocytes, as well as glucose-induced insulin secretion and the response to metabolic stress in β-cells, and in gluconeogenesis in hepatocytes. G3PP is a previously unknown player in metabolic regulation and signaling and offers a potential target for cardiometabolic disorders.