Intramuros' construction relied on local resources and artisans but initially struggled in defense. Weak fortifications and understaffed garrisons left it vulnerable to raids, notably by Chinese, Muslim, and Japanese pirates. Limahong, a notorious pirate, launched a devastating assault, inflicting heavy losses. Overcoming these challenges, Intramuros strengthened its defenses, transitioning from wooden palisades to stone structures after Legazpi's death in 1572, notably reinforced by Antonio Sedeño's efforts. By 1590, under Gomez Perez de Dasmariñas, it transformed into a fortified walled city, integrating Fort Santiago into its defenses along the Pasig River.

Intramuros strategically designed its defenses along Manila Bay and the Pasig River, encompassing 64 hectares within robust walls measuring 8 feet thick and 22 feet high. The fortifications underwent improvements in the 17th century, including the addition of walkways and reinforced stonework. However, a significant earthquake in 1645 necessitated extensive restoration efforts. The walled city featured nine bastions or baluartes, namely Baluarte de San Miguel, Medio Baluarte de San Francisco, Baluartillo de San Francisco Javier, Baluarte Plano Luneta de San Isabel, Baluarte de San Diego, Baluarte de San Andres, Baluarte de San Francisco de Dilao, Baluarte de San Gabriel, and Baluarte de Santo Domingo. Additionally, smaller fortifications like ravelins such as Revellin e Parian, Revellin de Real de Bagumbayan, and Revellin de Recolletos, as well as redoubts like Reducto de San Pedro and Reducto de San Francisco, enhanced the defensive capabilities of Intramuros.

Inside these walls stood iconic landmarks like Plaza Mayor, Ayuntamiento, Manila Cathedral, and Palacio del Gobernador, alongside numerous Roman Catholic churches. Despite challenges, Intramuros' architectural evolution, blending Spanish Mexican and arquitectura mestizo styles, laid the foundation for enduring Spanish Baroque aesthetics in the Philippines' historic churches today.