In the calidrine sandpiper red knot (Calidris canutus), the weeks preceding take off for long distance migration are characterized by a rapid increase in body mass, largely made up of fat but also including a significant proportion of lean tissue. Before take-off, the pectoral muscles are known to hypertrophy in preparation for endurance flight without any specific training. Because birds facing cold environments counterbalance heat loss through shivering thermogenesis, and since pectoral muscles represent a large proportion of avian body mass, we asked the question whether muscle hypertrophy in preparation for long distance endurance flight would induce improvements in thermogenic capacity. We acclimated red knots to different controlled thermal environments: 26°C, 5°C, and variable conditions tracking outdoor temperatures. We then studied within-individual variations in body mass, pectoral muscle size (measured by ultrasound) and metabolic parameters (BMR and summit metabolic rate, M_sum) throughout a three-month period enclosing the migratory gain and loss of mass. The gain in body mass during the fattening period was associated with an increase in pectoral muscle thickness and affected the change in thermogenic capacity independent of thermal acclimation. Regardless of their thermal treatment, birds showing the largest increases in body mass also exhibited the largest increases in M_sum. We therefore conclude that migratory fattening is accompanied by thermoregulatory side effects. The gain of body mass and muscle hypertrophy does improve thermogenic capacity independent of thermal acclimation in this species. Whether this represents an ecological advantage depends on the ambient temperature at the time of fattening.