Isoprenoid quinones constitute a class of redox lipids that are indispensable for electron transfer in a variety of cellular functions. For instance, plastoquinone, an integral component of plants, algae and Cyanobacteriota , plays a pivotal role in photosynthesis. Isoprenoid quinones are biosynthesised via evolutionary‐related pathways, in which some steps are still incompletely characterised. In this study, we confirm the identity of the PlqH enzyme, a flavin‐dependent monooxygenase (FMO) conserved in photosynthetic cyanobacteria, which possesses a regioselective hydroxylase activity required for plastoquinone biosynthesis. Phylogenetic analyses demonstrate that cyanobacterial PlqH homologues originated from FMOs involved in bacterial ubiquinone biosynthesis. The synthesis of plastoquinone by Escherichia coli was achieved by expressing two heterologous genes in a genetically engineered strain, which was optimised to produce plastoquinone levels comparable to those of natural ubiquinone. However, plastoquinone was unable to replace ubiquinone in several cellular processes in E. coli , suggesting that fine structural and thermodynamic constraints both play a significant role in the function of quinones.