Many long-distance migratory bird species are in decline, of which environmental changes, such as climate change and land-use changes, are thought to be important drivers. The effects of environmental change on the migration of these birds have often been studied during spring migration. Fewer studies have explored the impacts of environmental change on autumn migration, especially at stopover sites. However, stopover sites are important, as the quality of these sites is expected to change over time. We investigated impacts of local environmental conditions on the migration strategy and body condition of the Pied Flycatcher (Ficedula hypoleuca) at an autumn migration stopover site using long-term ringing data (1996–2018) and local environmental conditions. We found that although the arrival and departure dates of birds at the stopover site remained unchanged, the body condition (fat score) of the individuals caught decreased, and the stopover duration increased. This suggests that conditions at the stopover site during the autumn migration period have deteriorated over time. This study emphasizes the importance of suitable stopover sites for migratory birds and stresses that changes in environmental conditions during the autumn migration period may be contributing to the current decline in long-distance migratory passerines.