The lysosome/autophagy pathway maintains tissue homeostasis by degrading unwanted intracellular material and preventing energy crisis during nutrient starvation. Whether this catabolic pathway participate to cytoplasm remodeling during differentiation is incompletely understood. In my talk I will present data showing that chondrocyte differentiation, a mandatory event for bone formation, is associated to a transcriptional induction of lysosome biogenesis and autophagy. CRISPR/Cas9-mediated gene knock-outs combined to quantitative proteomic, phospho-proteomic and transcriptomic analyses demonstrated that this process is triggered by inhibition of the insulin/PI3K signaling pathway and activation of TFEB and TFE3, master transcription factors of lysosome biogenesis and autophagy. Notably, TFEB and TFE3 in chondrocytes induce degradation of Endoplasmic Reticulum (ER-phagy). Inhibition of ER-phagy, impairs TFEB-mediated ER-remodeling, secretome and differentiation in chondrocytes, and bone mineralization in Medaka fish. Taken together these data demonstrate that transcriptional regulation of lysosome biogenesis and autophagy participate to cell differentiation during organismal development.