Under his ministry, the church broadened the scope of its worship and increased the privileges of its pupils, but also turned back to Puritan tradition.

President of the college Increase Mather noted Pemberton "had a Pregnant Wit, and Strong Memory, and was a hard Student".

[1][3][2] He was a member of the Cambridge Association, a group of clergymen that met in the Harvard College library.

He received an offer from Charles Morton on November 23, 1694, to serve as minister at a church in Charlestown, but he declined, likely because he found himself too young.

Around the same time, Samuel Willard, then minister of the Old South Church, identified Pemberton as his potential successor.

[5] He was well-liked by the church, but sometimes angered his pupils for his liberal political views, which compelled him to prematurely readmit sinners to the covenant.

They believed that people should not have to provide anecdotal evidence of "religious experiences" to gain membership to the church, that all baptized adults should have the right to vote in ministerial elections, and that all children should be baptized so long as they have a Christian sponsor.

Benjamin Franklin, one of his subjects, recalled his absence and Sewall recorded his sickness on the 29th of September.

[1] Pemberton amassed a large collection of books over his lifetime, which was sold at auction after his death.