An energy decaying integration scheme for an intrinsic, geometrically exact, multibody dynamics model with composite, dimensionally reducible, active beamlike structures is proposed. The scheme is based on the first order generalized- method that was proposed and successfully applied to various nonlinear dynamics models. The similarities and the differences between the mathematical structure of the nonlinear intrinsic model and a parallel nonlinear mixed model of chains are highlighted to demonstrate the effect of the form of the governing equation on the stability of the integration scheme. Simple shape functions are used in the spatial discretization of the state variables owing to the weak form of the model. Numerical solution of the transient behavior of multibody systems, representative of various rotor blade system configurations, is presented to highlight the advantages and the drawbacks of the integration scheme. Simulation predictions are compared against experimental results whenever the latter is available to verify the implementation. The suitability and the robustness of the proposed integration scheme are then established based on satisfying two conservational laws derived from the intrinsic model, which demonstrate the retained energy decaying characteristic of the scheme and its unconditional stability when applied to the intrinsic nonlinear problem, and the dependance of its success on the form of the governing equations.