Recent tracking technologies have revealed remarkable diel flight altitude changes over the Sahara Desert in small migratory birds. However, the drivers and traits behind these strategies remain poorly understood, partly because few species and barriers have been studied. Using a dataset from 67 recovered multi-sensor loggers across 17 species, we examined how small landbirds cross two major marine barriers (the Bay of Biscay, the Mediterranean Sea) and the Sahara. We then used a comparative approach to test the influence of wing morphology, wing structure, and plumage color on flight altitude. Birds showed important differences across barriers: over the desert, they averaged 1,600 m at night and 2,800 m during prolonged daytime flights, while marine crossings occurred lower (750 m), sometimes just above water. Flight altitude increased with wing area, and species with shorter wing bones and darker plumage flew higher over the Sahara, likely to enhance heat dissipation and reduce solar heating. These findings refine hypotheses on barrier-crossing strategies and suggest broader ecological and evolutionary implications.