A volume-filtered Large-Eddy Simulation (LES) of oscillatory flow over a rippled mobile bed is conducted using an Euler-Lagrange approach. As in unsteady marine flows over sedimentary beds, the experimental data, referenced in this work for validation, shows quasi-steady state ripples in the sand bed under oscillatory flow. This work approximately reproduces this configuration with a sinusoidal pressure gradient driven flow and a sinusoidally rippled bed of particles. The LES equations, which are volume-filtered to account for the effect of the particles, are solved on an Eulerian grid, and the particles are tracked in a Lagrangian framework. In the Discrete Particle Method (DPM) used in this work, the particle collisions are handled by a soft-sphere model, and the liquid and solid phases are coupled through volume fraction and momentum exchange terms. Comparison of the numerical results to the experimental data show that the LES-DPM is capable of capturing the mesoscale features of the flow. The large scale shedding of vortices from the ripple peaks are observed in both datasets, which is reflected in the good quantitative agreement between the wall-normal flow statistics, and good qualitative agreement in ripple shape evolution. Additionally, the numerical data provides three insights into the complex interaction between the three-dimensional flow dynamics and bed morphology: (1) there is no observable distinction between reptating and saltating particle velocities, angular velocities or observed Shields parameters; (2) the potential motion of the mobile bed may create issues in the estimation of the bed shear stress used in classical models; and, (3) a helical pairing of vortices is observed, heretofore not known to have to have been identified in this type of flow configuration.