As small, flying, mammalian endotherms, insectivorous bats are adapted to operate at high levels of energy expenditure. In response to seasonally variable challenges, we predicted that bats should balance energy budgets by flexibly adjusting aspects of their physiology or behavior in ways that elevate metabolic capacity. We examined variation in energy storage and pathways for oxidative metabolism in Brazilian free-tailed bats (Tadarida brasiliensis) related to estimated costs associated with reproduction and migration. We collected pectoral muscle and liver from female T. brasiliensis at six time points during the summer and fall and measured changes in the activity of four enzymes involved with lipid metabolism. Body mass varied substantially with life-cycle stage, suggesting that rapid accumulation and use of fat stores occurs in response to current and anticipated energy demands. Catabolic enzyme activity (carnitine palmitoyl transferase [CPT], 3-hydroxyacyl-CoA dehydrogenase [HOAD], and citrate synthase [CS]) in the muscle was increased during lactation compared with early pregnancy but exhibited no change before fall migration. While there was no temporal change in lipid biosynthetic capacity in the liver, fatty acid synthase activity was negatively correlated with body mass. Variation in body mass and enzyme activity in T. brasiliensis during the summer suggests that stored energy is mobilized and lipid oxidative capacity is increased during periods of increased demand and that lipid biosynthetic capacity is increased with depletion of fat stores. These results suggest that bats are able to flexibly adjust metabolic capacity based on energy requirement to maintain energy balance despite high levels of expenditure.