An adaptive gain-scheduled flight control law is designed for a transport aircraft, within the context of the European project RECONFIGURE. A primary concern being on-line implementation, a recursive frequency domain estimator of the linearized aerodynamic model is developed, with a low on-line computational burden and the capability to track time-varying parameters. Next, an LFT flight controller is synthesized using a state-space modal technique, which depends on the model parameters to be estimated. Since the LFT controller online depends on the parameter estimates instead of the true values, its robustness to estimation errors needs to be assessed using μ and IQC analysis techniques. Full nonlinear simulations along a trajectory validate the good performance properties of the combined estimator and gain-scheduled flight controller.