Reduced-order modelling of multidisciplinary computational fluid dynamics can enable routine industrial gust load analysis. Key to the herein presented model reduction approach is that it modularly builds upon the widely accepted modal structural reduced-order model, where high-fidelity aerodynamics are simply projected onto the structural degrees-of-freedom, while opening a novel route to account for dominant modal aerodynamics in multidisciplinary edge-of-the-envelope flight physics. The influence of the flexible structure is captured by aeroelastic eigenmodes which originate in the structural equations. Such global aeroelastic modes for a large aircraft case with nearly 50 million degrees-of-freedom are computed for the first time using exact aerodynamics from computational fluid dynamics via the Schur complement method. The influence of atmospheric gusts is captured by modes from proper orthogonal decomposition applied to sinusoidal gust responses at discrete frequencies. Afterwards, the two sets of modes are combined and the linearised operator of the Reynolds-averaged Navier–Stokes equations coupled with a modal structural model is projected onto the resulting subspace. The constructed low-dimensional model can be solved rapidly for practical gust analysis giving accurate agreement with the full-order reference results throughout. Feasibility of aeroelastic model reduction, using the industry-grade computational fluid dynamics package DLR–TAU, for a relevant use case in transonic flight gust encounter is demonstrated.