Exercise is critical to metabolic health and contributes to the prevention of many metabolic diseases, including leading causes of mortality. Exercise induces a complex, coordinated response that targets signaling pathways across organs. These physiologic responses require marked changes in nutrient consumption, use, and production. Recent advances in stable isotope tracing and mass spectrometry allow for more comprehensive and quantitative characterizations of in vivo metabolism. Murine models recapitulate many of the metabolic responses to exercise observed in humans, while offering important advantages such as invasive tissue sampling and precisely controlled conditions between experiments. Here, I used steady-state infusions with isotope-labeled nutrients to provide a comprehensive depiction of fuel flux and contributions to tissue oxidation during acute exercise in fasted, fed, and exhausted female mice. I observed marked time and nutrient-dependent changes in nutrient flux. Exercise caused large increases in glucose fluxes generated from liver glycogen, lactate, and glycerol. This is an important species distinction from humans, who rely more on liver glycogen. I observed extensive glucose sparing by several tissue during exercise, especially in brown fat. Glucose-sparing broke down when mice reached exhaustion, despite concomitant hypoglycemia. Proteolysis and amino acid mobilization increased markedly, also an important divergence from humans. Fatty acids were the primary oxidative fuel during fasted exercise. Heart and muscle relied heavily on fatty acids to fuel their TCA cycles. Ketone production also rose with exercise duration and contributed to fuel oxidation across tissues. Ketogenesis was likely driven by a hepatic bottleneck caused by gluconeogenesis-induced cataplerotic stress. Novel changes in fuel consumption were observed in several unexpected organs, i.e. not directly involved in muscle contraction or fuel production, including the pancreas and brown fat. I also show the surprising persistence of substantial futile cycles, despite the energy costs of exercise. This data provides the first comprehensive and quantitative accounting of metabolism during exercise in an intact organism. These findings establish a foundation that will ultimately contribute to the development of new therapies targeting the prevention, management, and treatment of metabolic diseases.