The populations of many Afro-Palearctic migratory bird species have declined over the last 50 years, for reasons that remain poorly understood, but which could include major environmental changes in Africa. We mapped, for the first time, the aggregated population trends of migratory species onto their non-breeding distributions in sub-Saharan Africa and used regression models that account for non-stationarity to examine correlations between assemblage population trend indices and changes in climate and vegetation phenology over the same time period. This also allowed us to map geographical variation in relationships across Africa. Our results reveal that relationships between population trends of migrant bird species and climate and phenology are spatially highly variable, and that there are no consistent, flyway-wide associations between climate or phenology and population trends. However, we found evidence that migrant population changes may be more closely linked to indices of vegetation senescence and climate than to indices of greening, suggesting further lines of investigation. Simply using cumulative Normalised Difference Vegetation Index (NDVI) across Africa greatly underestimates the extent to which phenology and climate vary spatially, as do the relationships between population trends and these environmental variables. Furthermore, much better data on the non-wintering ecology and distributions of migrants, including connectivity between breeding and wintering grounds, are needed if we are to assess with any confidence the extent to which they may be impacted by changes in environmental conditions in Africa. Until then, we suggest that there is no simple relationship between migrant populations and NDVI across species' ranges, and that further studies should, at the very least, consider the multiple dimensions of phenology and the potential for spatial variation in relationships.