Nonlinear Moving Horizon Estimation (MHE) and Model Predictive Control (MPC) strategies for very flexible aircraft are presented. They are underpinned by a nonlinear reduced-order model built upon the structure’s natural modes of vibration. This internal model aims for a minimal realisation of the aircraft which retains sufficient information to enable efficient real-time estimation and control. It is based on a modal intrinsic description of geometrically-nonlinear beams and a linearised unsteady vortex lattice aerodynamic model. Numerical evidence has shown that models of this form are able to capture the main nonlinear geometrical couplings at a very low computational cost. This opens the door to MHE and MPC strategies, which are naturally more computationally demanding than other linear conventional strategies, but are more versatile and able to provide control in the usually neglected nonlinear regime. The proposed control framework is tested on models built in an in-house open-source nonlinear aeroelasticity simulation and analysis package, to emulate the controller performance on a realistic plant model. Very satisfactory results are obtained in a flutter suppression problem involving a very flexible clamped wing, where the nonlinearity of the problem is leveraged by the internal model to achieve stabilisation, and a payload drop control of a very flexible HALE aircraft.