Malays played a significant role in pre-Hispanic Philippine history. Malay involvement in Philippine history goes back to the Classical Era with the establishment of Rajahnates as well as the Islamic era, in which various sultanates and Islamic states were formed in Mindanao, the Sulu Archipelago, and around Manila.

Malays made large contribution to Philippine history, and influenced modern-day lifestyles of Filipinos. The Malay language was the lingua franca of the archipelago prior to Spanish rule due to the religious history of the Malay Archipelago.

Although the modern Philippines does not have a huge majority or minority of Ethnic Malays today, (Filipinos who identified as Ethnic Malay make up 0.2% of the total population), the descendants of Ethnic Malays have been assimilated into the wider related Austronesian Filipino culture, characterized by Chinese and Spanish influence, and Roman Catholicism, with others into the Moro Muslim population. Malay cultural influence is still strong in the culturally conservative regions of Mindanao, southern Palawan, the Sulu Archipelago, and to some extent in rural of the Visayas and Luzon, where much Malay involvement and intermixing came during the classical era.

In the modern day, the closest cultural population to Malays are the Moro peoples, the native Islamized populations of the Philippines that inhabit Mindanao, Sulu Archipelago, south Palawan, parts of Visayas and Metro Manila and its environs. They follow a culture and lifestyle somewhat similar to Malays (predominantly in dress code and religion), although this culturally differs in the areas that these groups follow traditions native to or unique to the Philippines, such as cuisine, traditional music, and language (which belong to the Visayan, Danao, and Sangiric branches of Philippine languages, and Sama-Bajaw languages). At present, Malay is spoken by a minority of Filipinos, particularly in Palawan, Sulu Archipelago and parts of Mindanao as a second language, mostly in the form of trade and creole languages, particularly Sabah Malay.

There is an often a lot of confusion in the Philippines between "ethnic Malays" and "Malay race", a term coined for brown-skinned Austronesian natives of not only the Philippines, but also of Malaysia, Indonesia, Brunei, Singapore and southern Thailand. The country had its own Malay nationalism, un-associated with the anti-colonial struggle in the British and Dutch East Indies. The Philippine nationalism occurred towards the end of Spanish occupation and was spearheaded by José Rizal. Unlike the Malay nationalism and "Malayness" in Indonesia which was defined by the ethnic group, and in Malaysia which was defined by Islam as well as being of the ethnic group, Rizal's movement was that of a secular vision to unify the natives of the Malay Archipelago and the Malay Peninsula, believing them to have falsely been divided by colonial powers.

Interaction between the natives of the Philippines and the Malay Srivijaya Kingdom (as well as the Javanese kingdoms of Majapahit and Medang) are recorded by the Laguna Copperplate Inscription, which dates approximately 900 A.D. This steel plate was written in a mix of Old Tagalog, Old Malay and Javanese. Among the Malays, the classical Philippine kingdoms also interacted with other native peoples of Indonesia, including the Minangkabau and Javanese.

The first-recorded Malay in Philippine history was Sri Lumay, although accounts him are mostly in Visayan folklore. Sri Lumay was born in Sumatra, an island in Indonesia with a high Malay-population, and was of mixed Malay and Tamil descent. He settled in somewhere in modern-day Visayas. Sri Lumay established the Rajahnate of Cebu. His sons also ruled nearby regions and kingdoms.

The name "Visayas" originates from the name "Srivijaya", the name of the aforementioned ancient Malay kingdom of the same that was centered in Sumatra and the Malay Peninsula.