In 1847, the 118 Relief Churches in Scotland formed a union with all the congregations of the United Secession Church and became the United Presbyterian Church. Therefore, the church on South College Street was renamed College Street United Presbyterian Church.
Overall, the middle of the 19th century was a period of significant change for Scottish religious life. The Great Disruption happened in 1843, during which 450 evangelical ministers separated themselves from the Church of Scotland and formed the Free Church of Scotland. The reason for the conflict echoed the disagreements that led to the formation of the Relief Church almost a century before. This time, the main conflict centred around whether the Church of Scotland or the British Government had the power to control clerical positions and benefits.
The Disruption led to the formation of two church congregations that later proved important for the South College Street church. Those two congregations were St John’s Free Church in the Pleasance, and the New North Free Church in the Cowgate.