Indirect noise is a significant contributor to aircraft engine noise, which needs to be minimized in the design of aircraft engines. Indirect noise is caused by the acceleration of flow inhomogeneities through a nozzle. High-fidelity simulations showed that some flow inhomogeneities can be chemically reacting when they leave the combustor and enter the nozzle (Giusti et al., Trans. ASME J. Engng Gas Turbines Power, vol. 141, issue 1, 2019). The state-of-the-art models, however, are limited to chemically non-reacting (frozen) flows. In this work, first, we propose a low-order model to predict indirect noise in nozzle flows with reacting inhomogeneities. Second, we identify the physical sources of sound, which generate indirect noise via two physical mechanisms: (i) chemical reaction generates compositional perturbations, thereby adding to compositional noise; and (ii) exothermic reaction generates entropy perturbations. Third, we numerically compute the nozzle transfer functions for different frequency ranges (Helmholtz numbers) and reaction rates (Damköhler numbers) in subsonic flows with hydrogen and methane inhomogeneities. Fourth, we extend the model to supersonic flows. We find that hydrogen inhomogeneities have a larger impact on indirect noise than methane inhomogeneities. Both the Damköhler number and the Helmholtz number markedly influence the phase and magnitude of the transmitted and reflected waves, which affect sound generation and thermoacoustic stability. This work provides a physics-based low-order model which can open new opportunities for predicting noise emissions and instabilities in aeronautical gas turbines with multi-physics flows.