This study sought to compare the behavior of Treg subsets displaying different coexpression patterns of Neuropilin‐1 (Nrp1) and Helios, under the influence of gut stress unrelated to hematopoietic stem cell transplantation, pretransplantation conditioning, and posttransplant gastrointestinal acute graft versus host disease (GI‐aGvHD). Host CD4+/CD25hi/Foxp3+ Treg cells, identified by flow cytometry, were isolated from various tissues of mice affected by these stressors. Expression of CD25, CTLA‐4, CD39, OX40, integrin‐β7, LAG3, TGFβ/LAP, granzyme‐A, ‐B, and interleukin‐10 was compared in four Treg subsets displaying Helios or Nrp1 only, both or none. Fluorescence‐activated cell sorter–sorted Treg subsets, displaying markers affected in a conditioning‐ and GI‐aGVHD‐restricted manner, were further investigated by transcriptome profiling and T‐cell suppression assays. We found that conditioning by irradiation greatly diminished the relative frequency of Helios+/Nrp1+ Treg, shifting the balance toward Helios−/Nrp1− Treg in the host. Upregulation of integrin‐β7 and OX40 occurred in GI‐aGvHD‐dependent manner in Helios+/Nrp1+ cells but not in Helios−/Nrp1− Treg. Sorted Treg subsets, confirmed to overexpress Nrp1, Helios, OX40, or integrin‐β7, displayed superior immunosuppressive activity and enrichment in activation‐related messenger RNA transcripts. Our data suggest that conditioning‐induced shrinkage of the Nrp1+/Helios+ Treg subset may contribute to the development of GI‐GvHD by impairing gut homing and decreasing the efficiency of Treg‐mediated immunosuppression.