The Protestant Church in Indonesia is the former East Indian State Church of the Dutch colonial era, a continuation of the church of the period of the East India Company in the 17th and 18th centuries. In 1835 Calvinist and Lutheran congregations came together in Batavia (Jakarta) to become the Protestant Church in the Netherlands East Indies. Its status was recognized by the colonial government in 1927.

The GPI is a corporate body which is now composed of twelve autonomous churches, four of which are members of the WCC in their own right:

• Evangelical Christian Church in the Minahasa (GMIM)
• Protestant Church in the Moluccas (GPM)
• Protestant Evangelical Church in Timor (GMIT)
• Protestant Church in Western Indonesia (GPIB).

The others are:

• Indonesian Protestant Church Gorontalo (GPIG) - 11,103 members
• Indonesian Protestant Church Donggala (GPID) - 30,114 members
• Indonesian Protestant Church Baggai Kepulawan (GPIBK) - 29,008 members
• Indonesian Protestant Church Papua (GPI-Papua) - 30,202 members
• Indonesian Protestant Church Buol Tolitili - 11,027 members
• Christian Church Luwuk Banggai (GKLB) - 42,611 members
• Evangelical Christian Church Talaud (GERMITA) - 14,734 members
• Indonesian Ecumenical Christian Church in California - 188 members

The congregations of the GPI are those of the autonomous churches. It is a corporate body which deals with issues on behalf of the twelve member churches and is responsible for some joint programmes. The leaders meet annually. Every five years a conference is held bringing together the delegates of the churches. The major concern of the GPI is to strive for closer ties between the regional churches, and for the unity of the church throughout Indonesia.