The Sierra Nevada de Santa Marta in northern Colombia has been identified as a critical spring stopover site for at least one Neotropical migratory bird species prior to crossing the Caribbean sea on migration. The strategic location of the Sierra suggests that other South American wintering migrants may stopover there, but no information is available on the migrant community during spring or how they distribute themselves between habitats and across the broad elevational gradient. Here, we present species richness and densities of migratory landbirds obtained through standardized census and captures along an elevation gradient (100–2,100 m) covering two habitats, forest and shade coffee, during two consecutive spring migrations. The migrant community (~39 species) showed a peak in species richness and abundance at mid elevations (700–1,700 m), mirroring the pattern often observed in communities of resident Neotropical birds. However, individually the abundance of the commonest species peaked at different elevations and showed high annual variability. We also found within-species differences in density between shade-coffee and forest at the same elevation, possibly reflecting differences in habitat quality for some species. Factors such as food availability and predation risk are expected to be critical in shaping the distribution of migrants during stopover, and further research is required to identify the drivers of the observed elevational patterns. This study contributes to our knowledge of the life histories of migrants during stopover and highlights the habitats and elevations where conservation measures would protect the highest number of species and individuals at a South American stopover site.