PCI partners with three churches in Indonesia: the Evangelical Christian Church in Halmahera (GMIH), the Evangelical Christian Church in Timor (GMIT) and the Christian Church of Sumba (GKS).

PCI also partners with the Communion of Churches in Indonesia (CCI/PGE).

The Evangelical Christian Church in Halmahera (GMIH) has around 160,000 members in an area that witnessed violence and bloodshed between the Muslim and Christian communities from 1999 to 2003. 

The Evangelical Christian Church in Timor (GMIT) is the second largest Protestant denomination with around 1.5 million members in Timor and 13 neighbouring islands. 

The Christian Church of Sumba (GKS) has seen constant growth since the 1980's.  Around 80% of the 550,000 inhabitants of the island of Sumba are Christians.

The Communion of Churches in Indonesia (CCI/PGE) acts on behalf of, and speaks for, more than 70 protestant churches, seeking to address national issues as they relate to Christians and their communities throughout Indonesia.