In January 1843 the government put a final negative on the church’s claims for spiritual independence. The non-intrusionist movement ended in the Disruption: on 18 May 1843, 470 clergy withdrew from the general assembly and constituted themselves the Free Church of Scotland, with Chalmers as moderator. He had prepared a scheme to fund the support of the seceding ministers.
In 1844, Chalmers announced a church extension campaign, for new building. In 1846 he became the first principal of the Divinity Hall of the Free Church of Scotland, as it was initially called.