Lipids are the dominant fuel source during migratory flight, but the factors controlling the relative importance of lipid, protein, and carbohydrate to flight metabolism remain unclear. I tested the nonexclusive hypotheses that diet, migration distance, or endogenous lipid reserves mediate variation in the fuels birds catabolize during migration. Blood plasma metabolite concentrations were significantly different among species, and indicated clear differences in protein and lipid utilization among three turdid chat and five sylviid warbler species caught during spring migration in the Negev Desert, Israel. Fruit-eating species (omnivores) catabolized less protein and more lipid during migration than insectivores. Metabolite concentrations of omnivorous Blackcaps (Sylvia atricapilla), Garden Warblers (S. borin), and Lesser Whitethroats (S. curruca) were consistent with low rates of proteolysis (low uric acid), and high rates of lipolysis (high free-fatty acid and β-hydroxybutyrate). On the other hand, metabolite concentrations of insectivorous Redstarts (Phoenicurus phoenicurus), Nightingales (Luscinia megarhynchos), Thrush Nightingales (L. luscinia), Barred Warblers (S. nisoria), and Orphean Warblers (S. hortensis) indicated increased proteolysis and decreased lipolysis. Blood metabolite concentrations, however, were not correlated with migration distance, and the results do not support the hypothesis that long-distance migrants use fuel differently than short-distance migrants. Triacylglycerol mobilization was positively correlated with the amount of visible subcutaneous fat, but blood metabolite composition was more strongly affected by diet. Omnivores and insectivores exhibit different fuel-use strategies to overcome the physiological challenges of migration.