In Ecuador, approximately 95% of existing buildings are low-rise residential structures of up to four stories, many of which were built informally and without compliance with current technical standards. Combined with the country’s high seismic hazard, this results in a significant seismic risk. This study presents a practical and replicable performance-based seismic design methodology for low-rise residential buildings. Five existing reinforced concrete frame structures with columns and spandrel beams, which withstood a recent severe seismic event without collapse, were analyzed. Comparative nonlinear analyses were conducted for models both excluding and including masonry infill walls, using the equivalent strut method and finite element modeling. Interstory drifts were calculated without masonry (maximum limit of 2%) and with masonry (maximum limit of 1%). The results show that masonry infill significantly reduces drifts and improves the seismic performance of the structural frame, preventing structural collapse, albeit at the cost of severe damage. Performance curves of the structures are presented, showing that the collapse prevention level is reached. Therefore, it is recommended that structural evaluations in Ecuador incorporate two analyses—with and without masonry infill walls—to ensure acceptable performance of both the structural skeleton and masonry walls. The proposed methodology, validated with at least two structural analysis software packages, is aimed at improving the evaluation of structures and the influence of masonry on structural performance.