The Spanish East Indies were the colonies of the Spanish Empire in Asia and Oceania from 1565 to 1901, governed through the captaincy general in Manila for the Spanish Crown, initially reporting to Mexico City, then later directly reporting to Madrid after the Spanish American Wars of Independence.

The king of Spain traditionally styled himself "King of the East and West Indies" (Spanish: Rey de las Indias Orientales y Occidentales).

From 1565 to 1821 these territories, together with the Spanish West Indies, were administered through the Viceroyalty of New Spain based in Mexico City. After independence of the Mexican Empire, Manila reported directly to Madrid. The territories ruled included present-day Philippines, Guam and the Mariana Islands, as well as Palau, part of Micronesia, and for a period Northern Taiwan and parts of North Sulawesi and the Moluccas (Dutch East Indies (VOC)). Cebu was the first seat of government when the Spanish first arrived in the Philippines, which was later transferred to Manila.

After the fall of Manila during the Spanish–American War in 1898, the United States occupied the city and the Spanish colonial government moved its capital to Iloilo, their strongest remaining stronghold in the Philippines. However, they soon surrendered the city to local revolutionary forces before American occupation. Spain later sold other smaller islands to Germany in the German–Spanish Treaty of 1899, and the few remaining islands were ceded to the United States when the Treaty of Washington was ratified in 1901.

With the Portuguese guarding access to the Indian Ocean around the Cape, a monopoly supported by papal bulls and the Treaty of Tordesillas, Spanish contact with the Far East waited until the success of the 1519–1522 Magellan–Elcano expedition that found a Southwest Passage around South America into the Pacific. The expedition reached the outskirts of the East Indies on 6 March 1521, sighting the Marianas. Upon reaching the Philippines, Magellan was able to convert and ally with Rajah Humabon, the Rajah of Cebu at that time, but died shortly thereafter in the Battle of Mactan while trying to shore up Humabon's control over nearby islands. When the expedition's new leaders refused to honor Magellan's will and free his Malay slave Enrique, Enrique—who also acted as their interpreter—was able to turn Humabon against them, provoking a massacre of the Spanish on 1 May. Consolidated onto the Trinidad and the Victoria, the survivors were able to reach the city-state of Tidore in the Spice Islands on 8 November. Its sultan Al-Mansur promptly pledged his realm as Spain's vassal the next day, hoping to use them as a counterweight to Portuguese support of his rival Bayan Sirrullah of Ternate. (Within a year, he was joined in this by Yusuf, sultan of Jailolo on nearby Halmahera.) However, by 14 May 1522 the Portuguese (under Antonio de Brito) forced Al-Mansur to surrender the Spaniards who had stayed in his realm and abjure any connection to Spain. The Victoria limped back to Spain to complete the first circumnavigation of the globe on September 6, and the Trinidad surrendered herself to de Brito to avoid starvation in November. Charles I signed away any remaining interests in the East Indies for 350,000 ducats in the Capitulation of Zaragoza on 22 April 1529.

Seeking to develop trade between the East Indies and the Americas across the Pacific Ocean, Antonio de Mendoza encouraged the exploration of these Asian territories and commissioned the expedition of his in-law Ruy López de Villalobos to the Philippines in 1542–1543. Miguel López de Legazpi set out from Mexico, and established the first Spanish settlement in the Philippines in 1565, which became the town of San Miguel in present-day Cebu. That same year, another member of the expedition, Andrés de Urdaneta, discovered a maritime route from the Philippines to Mexico, across the Pacific, leading to the important transpacific transport link of the Manila-Acapulco galleons.

In 1571, exploiting a rivalry between the states of Tondo and Maynila, the later being a city-state established by Bruneian Islamic colonists, meant to supplant Tondo, the Spaniards captured Maynila and renamed it Manila, a former satellite-state of the Brunei Sultanate and then Manila was made the seat of the Spanish Captaincy General of the Philippines. The Hindu Rajahnate of Butuan and the Kedatuans of Dapitan and Madja-as willingly joined the Spaniards to ally against their common Muslim rivals (Spain recently expelled the Muslims who invaded their homeland at the culmination of the Reconquista), Zamboanga was also taken from the Sultanate of Sulu via the efforts of Spanish and Peruvian soldiers and native allies as all these territories were incorporated into the Spanish East Indies.

The Philippines became the center of operations for further Spanish wars in Asia including the Castilian War against the Sultanate of Brunei, raids against the Ottoman protectorate of the Sultanate of Aceh, the brief conquests of the Sultanates of Tidor and Ternate as well as Spanish campaigns into Cambodia and Taiwan. These and other Asian territories claimed by the Spanish crown were to be governed from the Viceroyalty of New Spain in Mexico City.