Many species are becoming active earlier in the season as the climate becomes warmer. In parallel to phenological responses to climate change, many species have also been affected by habitat changes due to anthropogenic land use. As habitat type can directly affect microclimatic conditions, concurrent changes in climate and habitat could have interacting effects on the phenology of species. Temperature-related shifts in phenology, however, have mostly been studied independent of habitat types. Here, I used long-term data from a highly standardized monitoring program with 519 transects to study how phenology of butterflies is affected by ambient temperature and habitat type. I compared forests, agricultural areas and settlements, reflecting three major land use forms, and considered butterfly species that were observed in all three of these habitats. Seasonal appearance of the butterflies was affected both by the ambient temperature and the habitat type. As expected, warmer temperatures led to an overall advancement of the appearance and flight period of most species. Surprisingly, however, phenology of species was delayed in settlement habitats, even though this habitat type is generally associated with higher temperatures. A possible explanation is dispersal among habitat types, such that source–sink effects affect local phenology. When there is little productivity in settlement areas, observed butterflies may have immigrated from forest or agricultural habitats and thus appear later in settlements. My findings suggest that a spillover of individuals among habitats may affect phenology trends and indicate that phenological studies need to be interpreted in the context of habitat types. This becomes especially important when defining strategies to prevent or mitigate effects of climate and land-use changes on phenology and abundance of species.