Ecophysiology has enhanced our understanding of avian migration, yet many aspects of how these processes interrelate are still unclear. Partially migratory populations provide an ideal framework for its study in the wild, since resident and migratory individuals coexist temporarily in the same area, and face similar selection pressures. We focused on two Iberian populations of Eurasian hoopoe (Upupa epops), a trans-Saharan long-distance migrant, to explore the links between the immune system and migratory behaviour. We determined the migratory status of individual hoopoes using stable isotope analysis of deuterium (2H) and measured a number of immunological parameters, including estimates of innate and adaptive immunity, as well as body condition, and muscle and fat stores. Our results indicate that resident hoopoes had higher IgY levels and higher muscle and fat stores compared to migrants during the breeding season. Moreover, we found seasonal variation in leukocyte profiles of resident birds, with higher H/L ratios in winter than during the breeding season. We observed significantly higher H/L ratios and complement activity in resident males than in resident females, but not within migratory birds. Overall, we show differences in immune response linked to migratory behaviour in partial migratory populations. This study contributes to unraveling the associations between physiological status and migratory behaviour and ultimately helps to understand how different migratory strategies are maintained in partially migratory populations.