Using red knots (Calidris canutus) as a model, we determined how changes in mass and metabolic activity of organs relate to temperature-induced variation in metabolic performance. In cold-acclimated birds, we expected large muscles and heart, improved oxidative capacity and lipid transport, and we predicted that this would explain variation in maximal thermogenic capacity (M_sum). We also expected larger digestive and excretory organs in these birds and predicted that this would explain variation in basal metabolic rate (BMR). Knots kept at 5°C were 20% heavier and maintained 1.5 times more body fat than individuals kept at thermoneutrality (25°C). Cold-acclimated birds also had a BMR up to 32% higher and a M_sum 16% higher than birds at 25°C. Organs were larger in the cold, with muscles and heart being 9-20% heavier and digestive and excretory organs being 21-36% larger than at thermoneutrality. Rather than the predicted digestive and excretory organs, the cold-induced increase in BMR correlated with changes in mass of the heart, pectoralis and carcass. M_sum varied positively with the mass of the pectoralis, supracoracoideus and heart, highlighting the importance of muscles and cardiac function in cold endurance. Cold-acclimated knots also expressed upregulated capacity for lipid transport across mitochondrial membranes in their pectoralis and leg muscles, higher lipid catabolism capacity in their pectoralis muscles and elevated oxidative capacity in their liver and kidney. These adjustments may have contributed to BMR through changes in metabolic intensity. Our results also suggest indirect constraints on thermogenic capacity through limited cardiac capacity.