Although in the 1930s the government of the Dutch East Indies did not give its consent to the appointment of an overseas missionary in Bali, the Christian Church of East Java, without official approval, sent one of their ministers there. Through the Church of East Java, the mission of the Netherlands Reformed Church also participated in the work. By the thirties some congregations had emerged. During the second world war the congregations grew and new ones were formed so that they are now spread over a great part of the island. Although from the beginning no important decisions were taken without the consent of the delegates from the congregations, the church did not consider itself fully autonomous until 1948 when the first synod met.

Significant developments took place after 1950. The church contextualized the gospel in the local culture of Bali through architecture, symbols and teaching. Through traditional decoration, woodcarving, painting, dancing and music, the church is also engaged in the development programme of the government. In embodying the kingdom of God in Bali, the Protestant Christian Church in Bali is making Christ known to the people through its departments and institutions. The spiritual formation department is helping people to grow mature in spirituality. The diaconia department is assisting people to be self-sufficient economically. The work of the mission department is to provide people with education. The Dhyana Pura Institutions which look after Dhyana Pura Hotel, Dhyana Pura College and Wisma Nangun Kerti (guesthouse) are being used to help people live responsibly in the island of tourism.

The church has close ties with the Protestant Church in the Netherlands, the Evangelical Mission in South-West Germany, the Uniting Church in Australia, the United Church of Christ in USA, the Church of Westfalia in Germany and the Anglican Church in Australia.