There were at least two ways, however, in which Philippine Muslims were viewed as distinct from tribal groups by American colonial administrators. For one, although regarded as barbaric, Muslims were not considered savages as were tribal groups. This was due principally to their possession of both a world religion and an aristocracy. In line with the popular orientalism of the time and drawing on the experiences of earlier European colonizers in Muslim Southeast Asia, American colonizers often exhibited a certain respect for the "Mohammedanism" they found in the Philippines and did not encourage Christian proselytization among Philippine Muslims. Tribal groups on the other hand became a principal target for American Protestant missionaries. As one consequence of this attitude, American colonial administrators tended to conglomerate various Muslim ethnolinguistic groups under the single label "Moro" rather than focusing on the "tribal" divisions among them.

Secondly, unlike tribal Filipinos, Philippine Muslims were overwhelmingly lowlanders and were not exempted from the land registration and individual land ownership policies of the American colonial government. The Bureau of Lands conducted land surveys throughout Muslim areas and processed homestead applications. While there is some evidence to suggest that American colonial administrators believed that land registration would improve economic security for Muslim commoners, the actual application of American land policy led to the loss of traditional land rights for a great many Muslims (Thomas 1971).

With the establishment of the Philippine Commonwealth in 1935, government policy toward Philippine Muslims shifted significantly. The Bureau of Non-Christian Tribes was abolished in 1936 and with it the presumption that Muslims should be governed any differently, or afforded more protections, than any other citizens of the Commonwealth. This change in attitude was accompanied by a new policy priority: the economic development of Mindanao for the benefit of the nation, especially by means of Christian migration into traditionally Muslim regions.