The exceptional eggshell assemblage from Çatalhöyük was studied using an integrated approach combining morphology (by optical and scanning electron microscopy) and palaeoproteomics (by mass spectrometry). We provide taxonomic classification for 90 fragments, of which only 11 remain undetermined. The striking predominance of Anseriformes (probably including greylag geese, as well as ducks and swans) in all types of deposits examined, particularly middens and burial fills, suggests that these eggs were exploited as food and, at the same time, had a special significance for the inhabitants of the site. We detected the presence of crane eggshell in contexts associated with both the world of the living and the world of the dead (consistent with the well-known importance of this bird at Çatalhöyük), as well as the possible but infrequent occurrence of bustards and herons. Overall, we suggest that eggshell analysis, together with osteological data and the archaeological context, can provide the basis for a nuanced understanding of the relationship between humans and birds in the past.