After his stay in Mecca, Snouck was determined to go to the Dutch East Indies to study the Islamic society there. He managed to convince Minister of Colonies L.W.Ch. Keuchenius to send him to the colony for two years. In March 1889, he left Leiden for Batavia where he was commissioned to study Islam on Java. To do this, he travelled across the island, appointing Islamic scholars Sayyid Uthman and Haji Hasan Mustapa as his assistants. It was the beginning of a 17-year career as an adviser for Indigenous and Arab Affairs in the Dutch East Indies. During these years, Snouck provided the colonial government, including various local Dutch officials, with a lot of advice about

Islam in general, the application of Islamic law, how to deal with various Islamic matters and the best way to govern an Islamic population. He also had a major influence on the appointment of penghulus and chief penghulus in Java and elsewhere. In addition, he noted that Islam in the Dutch East Indies had its own character, with mysticism playing an important role. Various pre-Islamic customs and beliefs also persisted, but Indonesian Muslims were no less Muslim than Muslims elsewhere in the world. His statements on religious issues carried weight, even among Indonesian Muslims.