Mutual coupling of (thermofluiddynamic) modes of perturbations can affect the thermo-acoustic stability of combustors and contribute to combustion noise. For example, vortical or entropic perturbations can be transferred to acoustic perturbations if accelerated by the mean flow. The decomposition of perturbation fields into the respective modes and a linear description of their interactions in terms of fluctuating primitive variables is challenging. In contrast, Doak’s momentum potential theory promises an unambiguous decomposition in terms of momentum fluctuations, which is not limited to the linear regime. Whereas classical momentum potential theory takes into account hydrodynamic, acoustic and entropic modes in unconfined flows, the investigation of noise generation in combustion chambers requires the extension of the momentum potential theory to capture modes linked to the fluctuation of species mass fractions (“species mode”) arising from the change in chemical composition due to the reaction. Furthermore, a rigorous treatment of boundary conditions due to the confinement of the flow inside the combustor is required. The herein presented extension to reactive flows consists of two steps, (i) the formulation of a potential for momentum fluctuations related to species modes and (ii) identification of the total fluctuating enthalpy related to species modes. The extended theory is applied to post-process computational fluid dynamic simulation data of the propagation of entropy and species perturbations through one-dimensional ducts, nozzles and premixed flames. We find that although momentum potential theory offers a complete decomposition of momentum perturbations for reactive flows, the meaningful interpretation of this decomposition is rather challenging, even for non-reactive flows.