The MiT‐TFE family of basic helix‐loop‐helix leucine‐zipper transcription factors includes four members: TFEB, TFE3, TFEC, and MITF. Originally described as oncogenes, these factors play a major role as regulators of lysosome biogenesis, cellular energy homeostasis, and autophagy. An important mechanism by which these transcription factors are regulated involves their shuttling between the surface of lysosomes, the cytoplasm, and the nucleus. Such dynamic changes in subcellular localization occur in response to nutrient fluctuations and various forms of cell stress and are mediated by changes in the phosphorylation of multiple conserved amino acids. Major kinases responsible for MiT‐TFE protein phosphorylation include mTOR, ERK, GSK3, and AKT. In addition, calcineurin de‐phosphorylates MiT‐TFE proteins in response to lysosomal calcium release. Thus, through changes in the phosphorylation state of MiT‐TFE proteins, lysosome function is coordinated with the cellular metabolic state and cellular demands. This review summarizes the evidence supporting MiT‐TFE regulation by phosphorylation at multiple key sites. Elucidation of such regulatory mechanisms is of fundamental importance to understand how these transcription factors contribute to both health and disease.