In this study, a three-dimensional microscale framework utilizing the discrete element method (DEM) is presented to analyze the seismic response of soil–foundation–structure systems. The proposed approach is employed to investigate the response of a SDOF structure on a square footing founded on a dry granular deposit. The granular soil deposit is idealized as a collection of spherical particles using DEM. The spread footing is modeled as a rigid block composed of clumped particles and its motion is described by the resultant forces and moments acting upon it. The structure is modeled as a column made of particles that are either clumped to idealize a rigid structure or bonded to simulate a flexible structure of prescribed stiffness. Analysis is done in a fully coupled scheme in time domain while taking into account the effects of soil nonlinear behavior, footing embedment, possible separation between foundation base and soil due to rocking, possible sliding of the footing, and dynamic soil–foundation interaction as well as the dynamic characteristics of the superstructure. The impact of structure stiffness and damping, embedment of foundation, amplitude and frequency of input dynamic excitation on the response of the system for a specific set of conditions was examined. The relative contribution of base and lateral walls of the foundation to the total lateral response of the footing was evaluated. The analyzed system failed when the soil deposit with the flexible structure founded on a surface footing was excited with the resonance frequency of the structure. Uplift behavior of the footing associated with large rotation was observed in this condition. The computational approach is able to capture essential dynamic response patterns. For example, the lateral and rotational stiffness of foundation increased by embedding the foundation. The magnitude of permanent sliding, rotation, and settlement decreased as embedment depth increased.