He sympathised with Ebenezer Erskine, and the Commission of Assembly on 9 August 1733 suspended him and three associates from the exercise of their ministry.

Moncrieff with his brethren met at Gairney Bridge 6 December 1733, and formed the Associate Presbytery.

The Marrow Controversy, in which Thomas Boston of Ettrick was a conspicuous leader, began shortly after Moncrieff's ordination, and he joined the little band who were contending for purity of doctrine in the church.

The new denomination met with much sympathy and success, and was soon able not only to supply ordinances in different parts of the country, but even to organise a theological hall for the training of its future ministers.

In February 1742 Moncrieff was unanimously chosen professor of divinity, a position which he filled with great ability and zeal.

Moncrieff published in 1750 a vindication of the secession church, and in 1756 'England's Alarm, which is also directed to Scotland and Ireland, in several Discourses, which contains a warning against the great Wickedness of these lands/ A little devotional work by him, entitled 'A Drop of Honey from the Rock of Christ,' was published posthumously at Glasgow (1778).

With Erskine, William Wilson, and James Fisher he was joint author of the 'judicial testimony' against the church of Scotland, issued in December 1736.