Animal pollination is an important and highly valued ecosystem function and the role of birds as pollinators is increasingly acknowledged. However, such interactions can be challenging to document and often require extensive field programs. Over the last decade, environmental DNA (eDNA) has been analyzed from several different contemporary sample types, such as water, soil, flowers, and air. The applications of these studies include biodiversity monitoring, detection of endangered species, community compositions, and more recently, flower–arthropod interactions. However, it remains unknown whether flower eDNA is applicable to other taxonomic groups interacting with plants, as well as the deposition and degradation of eDNA on flowers. Here, we test whether eDNA from flowers can be used for detecting bird pollinators. In a controlled environment (an aviary with great tits [Parus major]), we show that birds leave significant traces of DNA on the flowers without observed visits (airborne eDNA). We further show that when birds had been in contact with the flowers, DNA concentrations increased to levels significantly higher than airborne background DNA. Subsequently, we sampled five clusters of wild flowers in Papua New Guinea and detected four species of birds, two of which are nectar-feeders, and one that is an insectivorous species known to visit flowers. These four bird species were regularly seen in the area and caught in mist-nets in the days prior to sampling of the flowers. In total, 29 bird species were recorded (18 mist-netted) in the area and of these, eight are nectarivorous. Our quantitative approach suggests that it is possible to distinguish airborne background bird DNA deposited on flowers from actual flower visits of birds in the wild, although this might be highly context-specific. Our findings are of broad interest within research on ecosystem functioning, biotic interactions, and plant–animal mutualism.