I develop an Effective Field Theory (EFT) framework to compute jet substructure observables for heavy ion collision experiments. As an illustration, I consider dijet events that accompany the formation of a weakly coupled Quark Gluon Plasma(QGP) medium in a heavy ion collision and look at an observable insensitive to jet selection bias: the simultaneous measurement of jet mass along with the transverse momentum imbalance between the jets that are groomed to remove soft radiation. Treating the jet as an open quantum system, I write down a factorization formula within the SCET(Soft Collinear Effective Theory) framework in the forward scattering regime. The physics of the medium is encoded in a universal soft field correlator while the jet-medium interaction is captured by a medium induced jet function. The factorization formula leads to a Lindblad type equation for the evolution of the reduced density matrix of the jet in the Markovian approximation. The solution for this equation allows a resummation of large logarithms that arise due to the final state measurements imposed while simultaneously summing over multiple incoherent interactions of the jet with the medium.