Tissue-resident memory CD8 T (TRM) cells serve as a front-line defense against microbial pathogens in barrier and mucosal tissues. Accurately predicting the roles of tissue-specific transcription factors (TFs) that regulate TRM biology remains a challenge. Here, by applying integrated transcriptomic and epigenomic analyses, we have identified an unexpected role for forkhead box O1 (Foxo1), a TF previously known to regulate circulating memory T cells, in intestinal TRM biology. Foxo1 repressed the maintenance of early small intestinal intraepithelial TRM cells in contrast with its actions in sustaining TRM cells from small intestinal lamina propria and colon and contrary to its broader role in promoting intestinal TRM cell formation. These findings highlight the emerging concept that the transcriptional regulation of TRM cells may be more complex and nuanced than previously appreciated and underscore the utility of integrated transcriptomic and epigenomic analyses in reconstructing TF-regulatory networks.