Agricultural intensification in Europe has affected farmland bird populations negatively, both during summer and winter. Although the migratory period poses separate challenges on birds than breeding and wintering, the consequences of farming practices for birds during migration remain poorly investigated. We monitored abundance and species richness of migratory birds in autumn at matched pairs of organic and conventional farms situated either in intensively farmed open plains (homogeneous landscapes) or in small-scale farming landscapes (heterogeneous landscapes) in southern Sweden. Total bird density did not differ between landscape types but was marginally higher on organic compared to conventional farms. When including taxonomic status in the model (passerines vs non-passerines), we found significantly more birds on organic farms, and more non-passerines in the homogeneous landscapes. The effect of farming practice and landscape type on density differed between functional groups. Omnivore density was higher in the homogeneous landscapes, and invertebrate feeders were marginally more abundant on organic farms. The effects of farming practice on the overall species richness and on the density of granivorous birds were landscape dependent. In the homogeneous landscapes, organic farms held a higher number of species and density of granivorous birds than conventional farms, but there was no such difference in the heterogeneous landscapes. Thus, organic farming can enhance abundance and species richness of farmland birds during migration, but the effect differs between landscape types and species. The effectiveness of organic farming was highest in the homogeneous landscape making it important to promote organic farming there. However, for some species during migration, increased heterogeneity in homogeneous landscapes may have negative effects. We propose that migratory bird diversity in homogeneous landscapes may be best preserved by keeping the landscape open, but that a reduced agricultural intensity, such as organic farming, should be encouraged.