Abstract Transition from an amorphous to a crystalline phase and stabilization of amorphous phases is a common strategy in biomineralization. Although no such phenomenon has yet been reported for biogenic calcium oxalate systems, it was recently demonstrated for synthetic calcium oxalate monohydrate (COM). Here we focused on COM raphides—needle shaped biominerals—synthesized by Duckweed. Although these raphides show some birefringence in polarized light, implying their crystallinity, they diffracted poorly when examined by x‐ray diffraction in our experiments. By means of transmission electron microscopy coupled with electron diffraction experiments we demonstrated that raphides from Duckweed are completely amorphous in their tip region and transform into a crystalline phase under the electron beam after a few seconds of exposure. To the best of our knowledge, this is the first report on biogenic amorphous calcium oxalate produced by a living organism.