Free vibration analysis of prestressed, homogenous, Fiber-Metal Laminated (FML) and composite beams subjected to axial force and end moment is revisited. Finite Element Method (FEM) and frequency-dependent Dynamic Finite Element (DFE) models are developed and presented. The frequency results are compared with those obtained from the conventional FEM (ANSYS, Canonsburg, PA, USA) as well as the Homogenization Method (HM). Unlike the FEM, the application of the DFE formulation leads to a nonlinear eigenvalue problem, which is solved to determine the system’s natural frequencies and modes. The governing differential equations of coupled flexural–torsional vibrations, resulting from the end moment, are developed using Euler–Bernoulli bending and St. Venant torsion beam theories and assuming linear harmonic motion and linearly elastic materials. Illustrative examples of prestressed layered, FML, and unidirectional composite beam configurations, exhibiting geometric bending-torsion coupling, are studied. The presented DFE and FEM results show excellent agreement with the homogenization method and ANSYS modeling results, with the DFE’s rates of convergence surpassing all. An investigation is also carried out to examine the effects of various combined axial loads and end moments on the stiffness and fundamental frequencies of the structure. An illustrative example, demonstrating the application of the presented methods to the buckling analysis of layered beams is also presented.