[1][2][3][4] Before the British invasion of Brunei and the Spanish invasion of the Philippines which placed the territory under the Mexico-governed Viceroyalty of New Spain, the Bruneian Empire was overlord over the Philippine kingdoms of the Sultanate of Sulu and the Rajahnate of Maynila as evidenced by the family connections between Rajah Matanda of Manila, Dayang-dayang (Princess) Mechanai of Sulu and Sultan Bolkiah of Brunei.

The said kingdoms had diplomatic relations with each other and the kings of these nations formed a regional Malay Muslim Royal clan which interconnected Malacca, Brunei, Pontianak, Samarinda, Banjarmasin, Manila and Sulu.

In even earlier times, according to the Yuan annals, "The Gazetteer of the South Sea" compiled during the Dade period of the Yuan Dynasty (Yuan Dade Nanhai zhi 元大德南海志) Brunei (Known as Poni) had alternatingly lost wars against or ruled over several Philippine kingdoms which included: Butuan 蒲端, Sulu سلطنة سولك, Ma-i 麻逸 (Mindoro), Malilu 麻裏蘆/षेलुरोङ् (present-day Manila), Shahuchong 沙胡重 (present-day Siocon), Madja-as otherwise known as Yachen 啞陳 (Oton), and Wenduling 文杜陵/سلطنة ماجينداناو (present-day Mindanao).

The Sultan met with Philippine President Rodrigo Duterte to discuss issues of mutual concern regarding peace and security.

[12] In 1983, there were approximately 8,000 Filipinos working in Brunei, with some of them involved in the construction of the Istana Nurul Iman and other projects of the Bruneian government.