In this work, a three dimensional multiscale formulation is presented for the analysis of masonry structures based on the multiscale finite element formulation. The method is developed within the framework of the Enhanced Multiscale Finite Element Method. Through this approach, two discretization schemes are considered, namely a fine mesh that accounts for the micro-structure and a coarse mesh that encapsulates the former. Through a numerically derived mapping, the fine scale information is propagated to the coarse mesh where the numerical solution of the governing equations is performed. Inelasticity is introduced at the fine mesh by considering a set of internal variables corresponding to the plastic deformation accumulating at the Gauss points of each fine-scale element. These additional quantities evolve according to properly defined smooth evolution equations. The proposed formalism results in a nonlinear dynamic analysis method where the micro-level state matrices need only be evaluated once at the beginning of the analysis procedure. The accuracy and computational efficiency of the proposed scheme is verified through an illustrative example.