Migratory birds encounter a large variety of parasites and pathogens en route and invest in immune defences to limit the risk and fitness costs of infection. Since both migration and immune defences carry costs, individuals on tight budgets may face trade‐offs between migratory progress and immune status. Many species alternate legs of strenuous migratory flight with stopovers during which birds refuel, rest, and recover physiologically. Despite this, most time and energy consumed during migration are actually spent on stopovers. As a result, identifying what determines stopover duration is key in understanding how migratory birds balance investments in immune defences and migration. Yet, it is unknown under what conditions an individual's immune status may affect migratory progress through the duration of stopovers. We explored whether immune status at arrival affects stopover duration by radio‐tagging and blood‐sampling common blackbirds Turdus merula during autumn stopovers on the Dutch island of Vlieland. To measure immune status, we quantified levels of bacterial killing ability, natural antibodies, complement, and haptoglobin, as well as heterophil–lymphocyte ratios. We show that stopover departures peaked during periods with low cloud cover and strong tailwinds. While lean birds prolonged stopovers, we only found a weak tendency of prolongation in birds with elevated haptoglobin levels. We conclude that effects of immune status on minimum stopover durations are subordinate to those of condition, cloud cover, and tailwinds in autumn‐migrating common blackbirds. Hence, future studies on the link between immune defences and stopover durations should take weather conditions into account.