Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention that involves a daily cycle of feeding and fasting. In both animals and humans, TRF has pleiotropic health benefits that arise from multiple organ systems, yet the molecular basis of TRF-mediated benefits is not well understood. Here, we subjected mice to isocaloric ad libitum feeding (ALF) or TRF of a western diet and examined gene expression changes in samples taken from 22 organs and brain regions collected every 2 h over a 24-h period. We discovered that TRF profoundly impacts gene expression. Nearly 80% of all genes show differential expression or rhythmicity under TRF in at least one tissue. Functional annotation of these changes revealed tissue- and pathway-specific impacts of TRF. These findings and resources provide a critical foundation for future mechanistic studies and will help to guide human time-restricted eating (TRE) interventions to treat various disease conditions with or without pharmacotherapies. Display omitted •80% of genes are differentially expressed or rhythmic under TRF in at least one tissue•TRF decreases genes involved in inflammatory signaling and glycerolipid metabolism•TRF increases genes involved in RNA processing, protein folding, and autophagy•TRF causes multi-tissue rewiring of BCAA, glucose, and lipid metabolism Deota et al. present a diurnal transcriptome atlas to map changes in response to time-restricted feeding (TRF) in 22 organs and brain regions. Under TRF, rhythmic gene expression increases across most tissues, and 80% of all genes show differential expression or rhythmicity in at least one tissue. TRF-induced feeding-fasting cycles lead to phase consolidation of anabolic and catabolic genes, improve metabolic flexibility, and cause multi-tissue rewiring of nutrient metabolism.