In 1683 Garden, already a D.D., became one of the ministers of the Kirk of St Nicholas, the parish church of New Aberdeen, where he continued until he was ‘laid aside’ by the privy council in 1692 for ‘not praying for their majesties,’ William III and Mary II.
He did not appear, and the Assembly deposed him and ‘prohibited him from exercising the ministry or any part thereof in all time coming.’ Garden paid no regard to the sentence, and continued to officiate as before to the members of his former congregation who adhered to episcopacy.
In 1703 he dedicated to Queen Anne, in terms of fervent loyalty to her, but with outspoken censure of the new presbyterian establishment, his magnificent edition of the works of Dr John Forbes (1593–1648) (Joannis Forbesii a Corse Opera Omnia), which was published at Amsterdam.
Introduced by the Earl of Mar, then secretary of state for Scotland, they were received with marked graciousness, and poured into her majesty's not unwilling ear (along with their thanks for the freedom they now enjoyed, ‘not only in their exercise of the pastoral care over a willing people, but also in their use of the liturgy of the church of England’—then a new thing among the Scottish episcopalians) their complaints of the persecution they had lately suffered, and their entreaties for a further measure of relief.
His Bourignianism, says George Grub doubtfully, was probably due to sheer weariness of the controversies wherewith his country had been so long distracted; moreover, his friend Henry Scougall had been in the habit of going to France as well as to Flanders for spiritual improvement.
His elder brother, James (1647–1726), minister successively of Carnbee (1678–81), New Machar in Aberdeenshire, Maryculter in Kincardineshire, and of Balmerino in Fife, became professor of divinity at King's College, Aberdeen, and was deprived in 1696 for refusing to sign the Westminster Confession of Faith.