In 1853 the Queensland Government granted of Crown land for a Presbyterian church, school and manse on the south-west corner of James Street and Hume Street (), now in East Toowooomba. In May 1858 tenders were called to erect a raised timber church of . By September 1858 construction had commenced but halted due to insufficient funds to complete the building. In March 1859 the Presbyterian minister at Ipswich, William Lambie Nelson, visited Toowoomba, spending a week successfully collecting funds to finish the church. The church building was finally completed on 11 September 1859 and was used by visiting ministers. It was not until 1863 that the congregation of St Stephen's was officially established when Nelson decided to purchase a farm in Toowoomba (now Gabbinbar) and became the Presbyterian minister at Toowoomba, preaching the first service on 6 December 1863.