Regulatory T (T_reg) cells respond to immune and inflammatory signals to mediate immunosuppression, but how the functional integrity of T_reg cells is maintained under activating environments is unclear. Here we show that autophagy is active in T_reg cells and supports their lineage stability and survival fitness. T_reg cell–specific deletion of Atg7 or Atg5, two essential genes in autophagy, leads to loss of T_reg cells, greater tumor resistance and development of inflammatory disorders. Atg7-deficient T_reg cells show increased apoptosis and readily lose expression of the transcription factor Foxp3, especially after activation. Mechanistically, autophagy deficiency upregulates metabolic regulators mTORC1 and c-Myc and glycolysis, which contribute to defective T_reg function. Therefore, autophagy couples environmental signals and metabolic homeostasis to protect lineage and survival integrity of T_reg cells in activating contexts.