This work contains a comparison between variational integrators and energy-momentum schemes for flexible multibody dynamics. In this connection, a specific “rotationless” formulation of flexible multibody dynamics is employed. Flexible components such as continuum bodies and geometrically exact beams and shells are discretized in space by using nonlinear finite element methods. The motion of the resulting discrete systems are governed by a uniform set of differential-algebraic equations (DAEs). This makes possible the application and comparison of previously developed structure-preserving methods for the numerical integration of the DAEs. In particular, we apply a specific variational integrator and an energy-momentum scheme. The performance of both integrators is assessed in the context of three representative numerical examples.