The mannose-6-phosphate (M6P) pathway is critical for lysosome biogenesis, facilitating the trafficking of hydrolases to lysosomes to ensure cellular degradative capacity [1], [2]. Fibroblast Growth Factor (FGF) signaling, a key regulator of skeletogenesis [3], has been linked to the autophagy-lysosomal pathway in chondrocytes [4], [5], [6], but its role in lysosome biogenesis remains poorly characterized. Here, using mass spectrometry, lysosome immune-purification, and functional assays, we reveal that chondrocytes lacking FGF receptors 3 and 4 exhibit dysregulations of the M6P pathway, resulting in hypersecretion of lysosomal enzymes and impaired lysosomal function. We found that FGF receptors control the expression of M6P receptors genes in response to FGF stimulation and during cell cycle via TFEB/TFE3 activation. Notably, restoring MPRs function—either through gene expression or activation of TFEB—rescues lysosomal defects in FGFR3;4-deficient chondrocytes. These findings uncover a novel mechanism by which FGF signaling regulates lysosomal function, offering insights into the control of chondrocyte catabolism and the understanding of FGF-related human diseases.