In flowers, anthocyanin pigments function as pollinator attractants, and in fruits, the colorful skins attract animals which will eat the fruits and disperse the seeds. In photosynthetic tissues (such as leaves), anthocyanins have been shown to act as a "sunscreen", protecting cells from photo-damage by absorbing UV and blue-green light, thereby protecting the tissues from photoinhibition, or high light stress. This has been shown to occur in red juvenile leaves, autumn leaves, and broad-leaved evergreen leaves that turn red during the winter. It is also thought that red coloration of leaves may camouflage leaves from herbivores blind to red wavelengths, or signal unpalatability to herbivores, since anthocyanin synthesis often coincides with synthesis of unpalatable phenolic compounds.

In addition to their role as light-attenuators, anthocyanins also act as powerful antioxidants, helping to protect the plant from radicals formed by UV light and during metabolic processes. This antioxidant property is conserved even after consumption by another organism, which is another reason why fruits and vegetables with red skins and tissues are a nutritious food source.