The development of self antigen‐specific T cells is influenced by how the self antigen is expressed. Here, we created a mouse in which a model self antigen is conditionally expressed in different tissue environments. Using peptide:MHCII tetramer‐based cell enrichment methods, we examined the development of corresponding endogenous self antigen‐specific CD4+ T cell populations. While ubiquitous self antigen expression resulted in efficient deletion of self antigen‐specific T cells in the thymus, some tissue‐restricted expression patterns resulted in partial deletion of the population in peripheral lymphoid organs. Deletion specifically affected Foxp3− conventional T cells (Tconv) with a bias towards high avidity TCR expressing cells in the case of thymic, but not peripheral deletion. In contrast, Foxp3+ Treg exhibited elevated frequencies with increased TCR avidity. T cells surviving deletion were functionally impaired, with Tconv cells exhibiting more impairment than Tregs. Collectively, our results illustrate how postthymic recognition of tissue‐restricted self antigens results in opposing developmental fates for Tconv and Treg cell subsets.