This study investigates the influence of the soil–structure interaction (SSI) on the seismic performance of structures, focusing on the effects of foundation size, soil type, and superstructure height. While the importance of SSI is well recognized, its impact on structural behavior under seismic loads remains uncertain, particularly in terms of whether it reduces or amplifies structural demands. A simplified dynamic model, incorporating both the mechanical behavior of the soil and structural responses, is developed and validated to analyze these effects. Using a discrete element approach and the 1940 El Centro earthquake for validation, the study quantitatively compares the response of soil-interacting structures to those with fixed bases. The numerical results show that larger foundation blocks (20 m × 20 m and 30 m × 30 m) increase the seismic response values across all soil types, causing the structure to behave more like a fixed-base system. In contrast, reducing the foundation size to 10 m × 10 m increases the flexibility of structures, particularly buildings built on soft soils, which affects the displacement and acceleration response spectra. Softer soils also increase natural vibration periods and extend the plateau region in regard to spectral acceleration. This study further finds that foundation thickness has a minimal impact on spectral displacement, but structures on soft soils show more than a 15% reduction in spectral displacement (SD) compared to those on hard soils, indicating a dampening effect. Additionally, increasing the building height from 7 to 21 m results in a more than 20% decrease in SD for superstructures with natural vibration periods exceeding 2.4 s, while taller buildings with longer natural vibration periods exhibit opposite trends. Structures built on soft soils experience larger foundation-level displacements, absorbing more seismic energy and reducing earthquake accelerations, which mitigates structural damage. These results highlight the importance of considering SSI effects in seismic design scenarios to achieve more accurate performance predictions.