In this research, a loop-separation concept (LSC) is applied to a very flexible aircraft. Appealing features of this control architecture include decoupled control logic and the use of high-order models for controller design, thus not requiring model order reduction. The LSC consists of two control loops. The inner loop employs a linear quadratic regulator capable of stabilizing the aircraft while controlling the shape of the half-wings independently from each other by artificially stiffening the structure. Structural dynamics can potentially be used in the design of the inner-loop regulator. The outer-loop design is based on rigid-body outputs. The outer loops for tracking velocity, heading, sideslip angle, and altitude are designed using nonsmooth H ∞ optimization techniques. Numerical results show that structural feedback in the inner loop yields better regulation performance and reduced structural deformations. The autopilot is capable of attaining the commanded reference with low control energy while meeting the maneuver requirements and regulating the elastic deformations of the wing.