It has been proved that using pure nonlocal elasticity, especially in differential form, leads to inconsistent and unreliable results. Therefore, to obviate these weaknesses, Eringen’s two-phase local/nonlocal elasticity has been recently used by researchers to consider the nonlocal size dependency of nanostructures. Given this, for the first time, the size-dependent nonlinear free vibration of nanobeams is investigated in this article within the framework of two-phase elasticity by using the Galerkin method. Contrary to differential nonlocal elasticity, the size dependency of the axial tension force, due to von Karman nonlinearity, is considered, and its effect on the nonlinear vibration is examined. The correct procedure of using the Galerkin method for studying the nonlinear vibration of two-phase nanobeams is introduced. It is shown that, although it is possible to extract the linear mode shapes of two-phase nanobeams using its equal differential equation, integral form of two-phase elasticity should be considered in the Galerkin method. Furthermore, it is observed that in two-phase elasticity, applying classic mode shapes in the Galerkin method leads to significant errors, especially in higher nonlocal parameters and lower values of local phase fraction and amplitude ratios.