In the year 1629, Portuguese Commander, Dom Miguel Noronha conquered Gangolli and built a fortress dedicated to St Michael and a church dedicated to the Immaculate Conception. But in 1630, it was re-dedicated to Our Lady of Immaculate Conception. Fr George de Concessao and Fr Francis Cordeiro of the Franciscan Order used to offer mass here. In 1757 the Portuguese had to leave Gangolli and the church was destroyed.

Chennammaji, the Queen of Keladi might have donated the place where the present church stands, to build a church. Blessed Joseph Vaz, the Vicar of the Kanara district (1681-1685) lived here and constructed the chapel. Fr Joachim Miranda (1759-1762), a Goan missionary known as Arkula Guru by the Hindus worked here before 1778. He was parish priest at Arkula church presently known as Omzoor. He had opened a Seminary at Monte Mariano. In about 1785 Tipu Sultan demolished the church. Gangolli was one of the five churches coming under Barcelore before 1816, dedicated to Nostra Senhora de Concessao, (Our Lady of the Immaculate Conception) a title still retained. The church was rebuilt after the return from captivity.

After 1812, Mr Louis D'Silva with the help of Rs 1,000/- (50% of it being aid given by Collector Harris) and the 8,000 stones from the Battery in Gangolli, began the construction of the church. Later with Rs 500/- collected as donation and another Rs 300/- by selling his wife's gold ornaments, he completed the church building. The church had a resident priest until 1845 when it began to be served from Kundapur of which it formed a part. From 1845 to 1902 nothing was heard about Gangolli as a separate parish. It was served from Kundapur. Fr Emmanuel Fernandes was appointed by Bishop Cavadini as the parish priest on March 10, 1902. He built the presbytery. Fr P.V. Gonsalves (1926-1937) constructed the Grotto. He also built a chapel at Padukone. Fr Paul D.G. Rego built the portico to the presbytery. Fr M.S. Menezes built the belfry with the donation from Mr Ignatius Almeida. In 1956, Fr Joseph D'Souza (1956-1962) renovated the church building, except the altar and facade, and also built a chapel at Trasi, which was served from Gangolli.