The Evangelical Christian Church in Halmahera (North Moluccas) grew out of the missionary work of the former Netherlands Reformed Church. It became autonomous in 1949. The church is organized according to the presbyterian-syn-odal model. In 1999-2000 and again in 2001, mass violence erupted in North Moluccas which caused death and destruction. People had to flee their homes and hide in the bushes, and many ended up as internally displaced persons in camps, in North Sulawesi and elsewhere. Although on a lesser scale, the tensions continue and people live in constant fear of provocation and terror. Widows and children are bearing the brunt of the conflict. They have to struggle for survival in conditions where there is very little access to basic necessities. The church has been severely affected by the situation. Its membership has decreased by more than half. It is trying to help its people in the congregations who have lost everything. The GMIH is convinced that the origins of the conflict were not religious but political, and that it was caused by forces from outside the area. Halmahera has become a province of its own, the Province of North Moluccas, with a Muslim majority. A Muslim-Christian working group has been set up and is working with the people to restore the relationships in the communities and bring back the normal conditions of daily life in the society. Displacement and resettlement have psychological and mental consequences for the population.

Since 1968 the GMIH operates its own theological college. It was moved from Ternate to Tobelo in 1989. The church is also related to the Theological Seminary in Ujung Padang (South Sulawesi).