One of the key issues in composite structures for aircraft applications is the early identification of damage. Often, service induced damage does not involve visible plastic deformation, but internal matrix related damage. A wide range of technologies, comprising global vibration and local wave propagation methods, can be employed for health monitoring purposes. Traditional modal analysis based methods are linear methods. The effectiveness of these methods is sometimes limited since they rely on a stationary and linear description of the system. The nonlinear interaction between a low frequency wave field and a local impact induced damage in a composite skin–stiffener structure is experimentally demonstrated in this work. The different mechanisms linked to the distorted waveforms are separated with the help of phase portraits. The harmonic waveform distortions are concentrated at the damaged region and increased for higher excitation amplitudes. It is shown that linear damage identification methods are feasible for low excitation amplitudes, but that the presence of nonlinear dynamic effects cannot remain silent for higher amplitudes. Analyzing the damage induced nonlinear effects can provide useful information about the current state of the structure.