The work presents a collaborative design approach, developed to account for the structure flexibility effects in the pre-design stages of generic aircraft configurations. A streamlined design process is developed between DLR and TU Delft, to support the transition from an initial aircraft conceptual solution, to physics based simulations. The TU Delft DEE initiator is the conceptual tool providing the initial design, which is used to instantiate further analysis tool. An Aeroelastic Engine module is responsible for the abstraction of the aircraft structural properties, and the generation of the fluid-structure disciplinary couplings, necessary to account for the flexibility effects. Multiple distributed disciplinary solvers are available, and accessible via a decentralized architecture. All the analysis modules are integrated in the design workflow by means of the open source distributed framework RCE, and the DLR’s central data model CPACS. The approach is tested for the pre-design of a conventional aircraft and a box-wing configuration, designed for a set of top level aircraft requirements. Hence, the flexibility effects for both cases are presented. The results demonstrate the importance of accounting for the flexibility effects already in the pre-design phase, especially in case of box-wing configurations, where difference in design performance can occur when ignoring such effects.