While natural CD4⁺Foxp3⁺ regulatory T (nT_REG) cells have long been viewed as a stable and distinct lineage that is committed to suppressive functions in vivo, recent evidence supporting this notion remains highly controversial. We sought to determine whether Foxp3 expression and the nT_REG cell phenotype are stable in vivo and modulated by the inflammatory microenvironment. Here, we show that Foxp3⁺ nT_REG cells from thymic or peripheral lymphoid organs reveal extensive functional plasticity in vivo. We show that nT_REG cells readily lose Foxp3 expression, destabilizing their phenotype, in turn, enabling them to reprogram into Th1 and Th17 effector cells. nT_REG cell reprogramming is a characteristic of the entire Foxp3⁺ nT_REG population and the stable Foxp3^NEG T_REG cell phenotype is associated with a methylated foxp3 promoter. The extent of nT_REG cell reprogramming is modulated by the presence of effector T cell-mediated signals, and occurs independently of variation in IL-2 production in vivo. Moreover, the gut microenvironment or parasitic infection favours the reprogramming of Foxp3⁺ T_REG cells into effector T cells and promotes host immunity. IL-17 is predominantly produced by reprogrammed Foxp3⁺ nT_REG cells, and precedes Foxp3 down-regulation, a process accentuated in mesenteric sites. Lastly, mTOR inhibition with the immunosuppressive drug, rapamycin, stabilizes Foxp3 expression in T_REG cells and strongly inhibits IL-17 but not RORγt expression in reprogrammed Foxp3⁻ T_REG cells. Overall, inflammatory signals modulate mTOR signalling and influence the stability of the Foxp3⁺ nT_REG cell phenotype.