How the formation and activity of CD4+Foxp3+ regulatory T cells (Tregs) is shaped by TCR recognition of the diverse array of peptide:MHC complexes that can be generated from self- and/or foreign Ags in vivo remains poorly understood. We show that a self-peptide with low (but not high) stimulatory potency promotes thymic Treg formation, and can induce conventional CD4+ T cells in the periphery to become Tregs that express different levels of the transcription factor Helios according to anatomical location. When Tregs generated in response to this self-peptide subsequently encountered the same peptide derived instead from influenza virus in the lung-draining lymph nodes of infected mice, they proliferated, acquired a T-bet+CXCR3+ phenotype, and suppressed the antiviral effector T cell response in the lungs. However, these self-Ag-selected Tregs were unable to suppress the anti-viral immune response based on recognition of the peptide as a self-Ag rather than a viral-Ag. Notably, when expressed in a more immunostimulatory form, the self-peptide inhibited the formation of T-bet+CXCR3+ Tregs in response to viral-Ag, and Ag-expressing B cells from these mice induced Treg division without upregulation of CXCR3. These studies show that a weakly immunostimulatory self-peptide can induce thymic and peripheral Foxp3+ Treg formation but is unable to activate self-Ag-selected Tregs to modulate an anti-viral immune response. Moreover, a strongly immunostimulatory self-peptide expressed by B cells induced Tregs to proliferate without acquiring an effector phenotype that allows trafficking from the draining lymph node to the lungs, and thereby prevented the Tregs from suppressing the anti-viral immune response.