Ebenezer's father, Henry Erskine, served as minister at Cornhill-on-Tweed, Northumberland, but was ejected in 1662 under the Act of Uniformity and imprisoned for several years.

[4] At the General Assembly of 1722, a group of men including Ebenezer had been rebuked and admonished for defending the doctrines contained in the book The Marrow of Modern Divinity.

After fruitless attempts to obtain a hearing, he, along with William Wilson of Perth, Alexander Moncrieff of Abernethy and James Fisher of Kinclaven, was suspended from the ministry by the Commission of Assembly in November of that year.

The Associate Presbytery remained united until 1747, when a division took place over how the church should respond to a new oath required of all burgesses.

This denomination, which continues today, operates Erskine College and Seminary in Due West, South Carolina.

He was Initiated in the Dunfermline Lodge of Free Gardeners in 1722 the same year as his patron, John Leslie, 8th Earl of Rothes.