We present a three-dimensional (3D) partitioned aeroelastic formulation for a flexible multibody system interacting with incompressible turbulent fluid flow. While the incompressible Navier–Stokes system is discretized using a stabilized Petrov–Galerkin procedure, the multibody structural system consists of a generic interaction of multiple components such as rigid body, beams and flexible thin shells along with various types of joints and connections among them. A co-rotational framework is utilized for the category of small strain problems where the displacement of the body is decomposed into a rigid body rotation and a small strain component. This assumption simplifies the structural equations and allows for the incorporation of multiple bodies (rigid as well as flexible) in the system. The displacement and rotation constraints at the joints are imposed by a Lagrange multiplier method. The equilibrium conditions at the fluid–structure interface are satisfied by the transfer of tractions and structural displacements via the radial basis function approach, a scattered data interpolation technique, which is globally conservative. For the coupled stability in low structure-to-fluid mass ratio regimes, a nonlinear iterative force correction scheme is employed in the partitioned staggered predictor–corrector scheme. The convergence and generality of the radial basis function mapping are analyzed by carrying out systematic error analysis of the transfer of fluid traction across the non-matching fluid–structure interface where a third-order of convergence is observed. The proposed aeroelastic framework is then validated by considering a flow across a flexible pitching plate configuration with serration at the trailing edge. Finally, we demonstrate the flow across a flexible flapping wing of a bat modeling the bone fingers as beams and the flexible membrane as thin shells in the multibody system along with the joints.