The late‐stage functionalization of indole‐ and tryptophan‐containing compounds with reactive moieties facilitates downstream diversification and leads to changes in their biological properties. Here, the synthesis of two hydroxy‐bearing allyl pyrophosphates is described. A chemoenzymatic method is demonstrated which uses a promiscuous indole prenyltransferase enzyme to install a dual reactive hydroxy‐bearing allyl moiety directly on the indole ring of tryptophan‐containing peptides. This is the first report of late‐stage indole modifications with this reactive group. The late‐stage functionalization of indole‐ and tryptophan (Trp)‐containing compounds with reactive moieties facilitates downstream diversification and leads to changes in their biological properties. The synthesis of two hydroxy‐bearing allyl pyrophosphates is described and a chemoenzymatic method is demonstrated which uses a promiscuous indole prenyltransferase (IPT) enzyme to install a dual reactive hydroxy‐bearing allyl group directly on the indole ring of tryptophan‐containing peptides.