This work investigates the propeller’s influence on the stability of High Altitude Long Endurance aircraft, incorporating all resultant loads at the propeller hub, propeller slipstream, and gyroscopic loads. Such effects are usually neglected in the aeroelastic simulation of HALE aircraft. For that goal, a previously developed framework, which couples a geometrically nonlinear structural solver with an Unsteady Vortex Lattice method (uVLM) for lifting surfaces and a Viscous Vortex Particle (VVP) method for propeller slipstream, was employed to generate time-data series. Also, a method, based on a combination of Proper Orthogonal Decomposition and system identification, to extract dynamic information (frequencies, damping, and modes) of the aircraft from a time-series signal is proposed and successfully tested for a purely structural case, for which reference data is available. The method is then applied to investigate the stability of aeroelastic cases. The results demonstrate that the presence of propellers can influence the aeroelastic stability of a Very Flexible Aircraft.