All the fruits that are or were green accumulate phyllobilins, which are the terminal chlorophyll catabolites. Phyllobilins are part of our daily diet, however, only a few structures have been identified in edible species. To unravel the phyllobilin biosynthetic pathway in fruits, a robust database with 956 phyllobilins was built and taking advantage of our metabolomic approach, three new phyllobilins were identified in melon fruits. Two of them were hydroxylated, an unprecedented biosynthetic pattern in fruits. Even more, one phyllobilin was dihydroxylated for the first time, and the other phyllobilin was a hydroxylated YCC. The third new phyllobilin identified in melon fruits was a pyro-phyllobilin, a long-sought structure that has been kept elusive until now. Therefore, two new biochemical pathways are unravelled to complement the current knowledge of the chlorophyll degradation pathway. Three new phyllobilins with potential health properties also increase the pool of phytochemicals in edible fruits.