Migration is a physiologically demanding activity. Recent studies suggest that migrating birds can improve their immune and antioxidant status during stopover, implying that variation in stopover habitat can affect migrants' health. We studied 2 species that are strongly frugivorous during fall migration, Swainson's Thrushes (Catharus ustulatus) and Gray Catbirds (Dumetella carolinensis). We asked whether birds that used shrubland dominated by exotic plants experienced differences in mass change, immune function, and antioxidant status relative to conspecifics in native-dominated shrubland during fall stopover in Michigan, USA, in 2012–2013. We found no habitat-related differences in any of the measured health parameters for Swainson's Thrushes. However, Gray Catbirds using native-dominated shrubland retained mass while those in exotic-dominated shrubland lost mass in 2013. Gray Catbirds in exotic-dominated habitat that year also had poorer immune status (elevated granulocyte:lymphocyte ratio and reduced hemagglutination and haptoglobin) and had lower plasma total carotenoids (immunostimulatory antioxidants) relative to conspecifics in native-dominated shrubland. While these findings were not replicated in 2012, circulating antioxidant capacity was lower in both years in Gray Catbirds captured in exotic habitat. Habitat-specific estimates of dietary energy, carotenoid, and antioxidant content per unit mass of fruit were similar between habitat types for Swainson's Thrushes. For Gray Catbirds, however, the fruit diet was lower in carotenoids and antioxidant capacity, but not in energy, in exotic habitat. Our results provide evidence that differential use of stopover habitats may affect the immune and antioxidant status of migrating landbirds. Furthermore, our results suggest that habitat may affect health status based on the complex relationships among quality and abundance of food, food preferences, and refueling performance, which vary among species. We suggest that future studies measure immune and antioxidant metrics in addition to refueling performance to better understand the effects of stopover habitat use on landbird migrant health. This information may improve assessment of habitat quality for migrants.