[3] El Morro, alongside La Fortaleza, San Cristóbal, El Cañuelo, and other forts part of the Walls of Old San Juan, protected strategically and militarily important Puerto Rico, or La Llave de las Indias (The Key to the Indies),[4] from invasion by competing world powers during the Age of Sail.

[7] The original fortress was built under the direction of conquistador Diego Ramos de Orozco and its main purpose was to defend the port of San Juan by controlling the entry to its harbor.

San Juan construction began in March 1589 with skilled artisans, 12 stonecutters, 18 masons, 2 smiths, a cooper, metal founder, and an overseer assigned to the task, with the help of 150 slaves.

[8]: 54–55, 59–61, 64–65 The top of the Castillo de San Felipe del Morro Lighthouse was destroyed during the 1898 bombardment of the city by the United States, and the American flag replaced the Spanish on 18 November 1898.

[8]: 78 [6]: 163 Upon the advice of Gonzalo Fernández de Oviedo y Valdés, a battery was constructed on the rocky promontory called "the Morro", when the location of La Fortaleza was deemed unsuitable.

[9][8] During the Spanish government of the island, El Morro, also known as Castillo de San Felipe, survived several attacks from foreign powers on various occasions.

In 1593 Portuguese soldiers, sent from Lisbon by order of Phillip II, composed the first garrison of the San Felipe del Morro fortress in Puerto Rico.

El Morro managed to resist the siege and eventually made the Dutch retire, although the attackers were able to sack and burn the city before leaving the Battle of San Juan (1625).

In 1797, British General Ralph Abercromby and Admiral Henry Harvey, with a force of 7,000–13,000 men, invaded the island of Puerto Rico.

The war ended with the signing of the Treaty of Paris, in which Spain ceded ownership of the islands of Puerto Rico, Cuba, Guam, and the Philippines to the United States.

El Morro and many other Spanish government buildings in Old San Juan became part of a large U.S. Army post, called Fort Brooke.

During World War II the United States Army added a massive concrete bunker to the top of El Morro to serve as a Harbor Defense Fire Control Station to direct a network of coastal artillery sites, and to keep watch for German submarines which were ravaging shipping in the Caribbean.

In honor of the Quincentennial of the voyages of Columbus in 1992 the exterior esplanade was cleared of palm trees that had been planted by the U.S. Army in the Fort Brooke era, and restored to the open appearance this "field-of-fire" for El Morro's cannon would have had in colonial Spanish times.

Puerto Rico as such was considered by the Spanish crown as the "Key to the Antilles"; no enemy ship could navigate its waters without fear of capture.

Following concerns over an increase in their population, in 2023 the National Park Service announced it would contract an animal welfare organization to remove the cats and threatened to hire a pest control agency if it were to fail.