To date, macroinvertebrates such as worms, clams, crustaceans, and insects have been considered the principal prey of shorebirds. However, such prey cannot account for their complete diet. Here, we conducted field observations on shorebird foraging behavior on Japanese and Canadian tidal flats, analyzed chemical components of the bird droppings and prey items. One of the surprising discoveries is that many shorebird species, such as Dunlin (a very common species worldwide) and Red-necked Stint (very common in East Asia and Oceania), consume surficial intertidal biofilm, a hitherto unsuspected food comprised of microbes, their extracellular mucus substances, and detritus. This finding is the first in the world to demonstrate that biofilm feeding is indeed widespread. We estimate that the contribution of biofilm to total diet is up to 70%. Also, we revealed that the determinants of shorebird reliance of biofilm include shorebird body size, foraging rate, and phylogeny as well as biofilm density. Biofilm feeding by shorebirds means that “a critical missing link” between birds and biofilm in intertidal flat ecosystems has now been identified, which revises shorebirds’ trophic position and reveals new food web structures. Food web theory predicts that the biofilm-shorebird link stabilizes the food web structures and supports a persistent coexistence of basal species (biofilm), consumers (invertebrates), and predators (birds). Thus, declines in shorebird populations raise an alarm for far-reaching effects on the stability of whole ecosystems. This study can assist in recovering worldwide declines in shorebird biodiversity as well as conservation and restoration of the integrity of intertidal flat ecosystems. We propose ideal configurations applied to the planning and designing of intertidal flat restoration projects, in the light of benefits from ecosystem services provided by shorebirds.