At that time the Welsh nonconformists of every denomination were seething with theological controversies, and it was not long before the ministry of Michael Jones provided the setting for one of the fiercest of these — the ‘ Controversy of the Systems ’ as it was called. Ever since the days of George Lewis the Presbyterian ‘system’ had operated in the Old Chapel , and this was the cause of the whole bitter struggle. Interwoven with this question of church government were various doctrinal disputes such as those between Higher and Lower Calvinists . In consequence, the church was split into two parties — Michael Jones 's party and the ‘Old People's’ party. He was accused of ignoring the principle of Presbyterianism in the government of the church, of being an Arminian , of denying Original Sin, of putting his trust in the ‘power of man,’ and of affirming the universality of Redemption.

On 11 Nov. 1821 the ‘Old People’ left the church; other ministers were called in to attempt to bring about a reconciliation, and, after they had failed in their efforts, a law-suit was started for possession of the chapel. The ‘Old People’ won, and Michael Jones and his party left the Old Chapel for nearly ten years, during which time they worshipped at his home at Weirglodd Wen , whither he had moved from the manse. In 1839 the two parties were reconciled and he moved back to the chapel.

In 1842 Michael Jones went to Bala to take charge of a new seminary for the training of young candidates for the ministry — this was later known as the Independent College . It had been started originally in 1841 at Weirglodd Wen , Llanuwchllyn , where he also kept one of Dr. Daniel Williams 's schools. He d. 27 Oct. 1853 , and was buried at Rhosyfedwen , the Old Chapel burial ground.