In 1903, the main secular Acehnese resistance leaders including Sultan Muhammad Daud, Tuanku Raja Keumala, Mahmud and Muda Perkasa capitulated.

The Dutch consolidated their control over Aceh by practising a policy of religious tolerance as a means of dissuading the Acehnese from taking up an armed struggle.

In the Netherlands at the time, Van Heutsz was considered a hero, named the 'Pacifier of Aceh' and was promoted to become governor-general of the entire Dutch Indies in 1904.

The Dutch establishment defended its actions in Aceh by citing a moral imperative to liberate the masses from the oppression and backward practices of independent native rulers that did not meet accepted international norms.

Colonial influence in the remote highland areas of Aceh was never substantial, however, and limited guerrilla resistance led by religious ulema persisted until 1942.

One intellectual Sayyid Ahmad Khan advocated discontinuing the "jihad" against the Dutch since the term was used to define military warfare against religious oppression.