This study investigated the impact of soil-structure interaction on multi-degree-of-freedom structures using the shallow-foundation Winkler model, known as the BNWF model. The model’s period was determined through eigenvalue analysis and compared to results obtained from FEMA’s formula. Results indicated that considering the soil, the structure’s period increased by up to 8.7% compared to the fixed-base model, aligning with FEMA’s calculations. Furthermore, with adequate ground acceleration, roof displacement increased by 3.4% to 3.8%, while base shear decreased by 4% to 10%. However, roof displacement and base shear increased in some earthquake scenarios due to spectral shape effects in regions with extended structural periods. Foundation damping effects, determined through the foundation’s moment-rotation history, grew with higher ground acceleration. This suggests that accounting for period elongation and foundation damping can enhance the seismic design of multi-degree-of-freedom structures.