For the most part of the Philippines' history, the region and most of Mindanao has been a separate territory, which enabled it to develop its own culture and identity. The region has been the traditional homeland of Muslim Filipinos since the 15th century, even before the arrival of the Spanish who colonized most of the Philippines beginning 1565. Arab missionaries arrived in Tawi-Tawi in 1380 and started the conversion of the native population into Islam. In 1457, the Sultanate of Sulu was founded and not long after were the sultanates of Maguindanao and Buayan established. At the time when most of the Philippines was under Spanish rule, these sultanates maintained their independence and regularly challenged Spanish domination of the Philippines by conducting raids on Spanish coastal towns in the north and repulsing repeated Spanish incursions in their territory. It was not until the last quarter of the 19th century that the Sultanate of Sulu formally recognized Spanish sovereignty, however these areas remained loosely controlled by the Spanish as sovereignty was only limited to military stations and garrisons and pockets of civilian settlements in Zamboanga and Cotabato, until they had to abandon the region as a consequence of their defeat in the Spanish-American War.

In 1942, during the early stages of Pacific War the Japanese Imperial Forces invaded and overran Mindanao and the ARMM. 3 years later, in 1945, United States and Filipino troops landed in Mindanao, and, with the help of local Filipino guerrillas, ultimately defeated the Japanese forces occupying the region.