Currently, the usefulness of proper orthogonal decomposition (POD) is limited to computational domains with fixed meshes and fixed boundaries. This paper presents a new POD method that enables the modeling of flow through computational domains with deforming meshes and/or moving boundaries. To achieve this goal, the solution is approximated using basis functions which, although not explicitly functions of time, depend on parameters associated with flow unsteadiness. Results are shown for transonic flow through the Tenth Standard Configuration. Comparisons are made between this method and the standard approach for on- and off-reference flow conditions. This method properly captured flow nonlinearities and shock motion for cases in which the classical POD method failed.