The paper proposes a decoupled identification approach for determining unknown parameters of a flexible aircraft. The methodology relies on an input-output transformation designed to excite only certain parts of the dynamics. Accordingly, a simplified Single Input Single Output (SISO) model is obtained, where an additional disturbance term is introduced for the neglected dynamics. Besides being a SISO problem, the decoupling transformation also scales down the numerical complexity of the identification problem by reducing the dimension of the unknown parameter vector. A well-known output error minimization can then be carried out either in batch or in real-time operation, where the introduced error due to the neglected dynamics can be directly incorporated in the characterization of the parameter estimation’s goodness through bounding ellipsoids. A comparative numerical example is given based on a reduced order linear time invariant (LTI) model of an experimental aircraft developed in the FLIPASED project.