The mechanistic target of rapamycin kinase complex 1 (mTORC1) is a key signaling hub that acts as a central regulator of several cellular processes, including cell growth and metabolism. The activation of mTORC1 occurs at the lysosomal surface via a two-step mechanism that requires a) its amino acid-dependent recruitment to the lysosome via the Rag GTPases and b) its growth factor-dependent activation by Rheb. mTORC1 senses and integrates multiple upstream signals to phosphorylate a broad number of substrates and modulate the crucial balance between cell anabolism and catabolism. However, whether mTORC1 can differentially regulate specific proteins to selectively respond to such a variety of intracellular and environmental cues is poorly understood. Here we show that Transcription Factor EB (TFEB), a master modulator of lysosomal biogenesis and autophagy, is modulated by mTORC1 via a specific substrate recruitment mechanism that is mediated by Rag GTPases. Differently from the well-characterized mTORC1 substrates S6K and 4E-BP1, which are recruited by mTORC1 via binding to the regulatory subunit Raptor, TFEB interaction with mTORC1 relies on its physical association with active Rag C/D. Owing to this mechanism, TFEB phosphorylation is insensitive to growth factor-mediated activation of Rheb but highly sensitive to amino acid-mediated activation of Rag GTPases. Strikingly, substituting the region of TFEB responsible for its recruitment to mTORC1 with the one of S6K, inverted TFEB phosphorylation behaviour and made it similar to S6K/4E-BP1. Thus, our findings reveal that diversity in mTORC1 substrate recruitment mechanisms enables mTORC1 to induce selective responses to specific nutritional cues.