He was an ardent theological student, a man of warm feelings and considerable mental powers, and he soon came prominently forward as the leading apologist of the new doctrine, winning his spurs in a controversy with one William Mitchell. The publication of fifteen Theses Theologiae (1676) led to a public discussion in Aberdeen, each side claiming a victory. The most prominent of the Theses was that bearing on immediate revelation, in which the superiority of this inner light to reason or scripture is sharply stated. His greatest work, An Apology for the True Christian Divinity, was published in Latin at Amsterdam in 1676, and was an elaborate statement of the grounds for holding certain fundamental positions laid down in the Theses. It was translated by its author into English in 1678, and is claimed to be "one of the most impressive theological writings of the century."
Barclay experienced to some extent the persecutions inflicted on the Quakers, and was several times thrown into prison. He travelled extensively in Europe (once with Penn and George Fox), and had several interviews with Elizabeth, princess palatine.
In later years he had much influence with James II, who as duke of York had given New Jersey to Sir George Carteret and John Berkeley, 1st Baron Berkeley of Stratton. After Carteret's death his half (East Jersey) was sold in 1682 to twelve people, eleven of whom were members of the Society of Friends. One of the eleven Quaker proprietors was William Penn, and after expanding to include a larger number of proprietors, the group elected Barclay to be the governor. He is said to have visited James with a view to making terms of accommodation with William of Orange, whose arrival was then imminent. He died on the 3rd of October, 1690.