AbstractImmune cells must adapt to different environments during the course of an immune response. Here we study the adaptation of CD8⁺ T cells to the intestinal microenvironment and how this process shapes the establishment of the CD8⁺ T cell pool. CD8⁺ T cells progressively remodel their transcriptome and surface phenotype as they enter the gut wall, and downregulate expression of mitochondrial genes. Human and mouse intestinal CD8⁺ T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We find that the intestinal microenvironment is rich in prostaglandin E₂ (PGE₂), which drives mitochondrial depolarization in CD8⁺ T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE₂ sensing promotes CD8⁺ T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell pool. Thus, a PGE₂-autophagy-glutathione axis defines the metabolic adaptation of CD8⁺ T cells to the intestinal microenvironment, to ultimately influence the T cell pool.