The earliest services in Boonah were Presbyterian Services held in the old Dugandan Homestead at the invitation of Mr Macquarie MacDonald. A request from Mr MacDonald to the Church of Scotland brought the Rev. W,L. Nelson to Ipswich in 1853. He preached occasionally at Dugandan from that time. Other Ministers followed and the practice continued somewhat irregularly until Mr. Edward Smythe arrived in January 1915 as the first Presbyterian Missionary. Two months later the stump capping ceremony of St Thomas’ Church was conducted by Rev. Peter Robinson in Ipswich who has preached his first sermon at Dugandan in 1871 and who, in 1889, had received for the Church, from Mr Cambell MacDonald, a gift of land on which the Church was to be built.
In 1925 the Presbyterian Church purchased for a Manse the old home of the late Mr & Mrs Haygarth. This home was next to the Church. Mrs. Haygarth has been Mary Jesse MacDonald of Dugandan. She was born on September 14th, 1844, the first white child born in the Fassifern.
Although the Congregational Church was never established in Boonah it did maintain a Church nearby at Coulson from 1879 – 1954, with a ministry from Peak Crossing.