Although not entirely accepting of the Church of England's ecclesiastical practices, Perkins conformed to many of the policies and procedures imposed by the Elizabethan Settlement.

In addition to writing, he also served as a fellow at Christ's College and as a lecturer at St. Andrew's Church in Cambridge.

[4] His family was evidently of some means, since in June 1577, at age 19, Perkins was enrolled as a pensioner of Christ's College, Cambridge[5] being trained in the tradition of the Reformed scholastic framework.

[6] Thomas Fuller's biographical profile of Perkins portrayed him as "very wild in his youth," skilled in mathematics, possessed of "a rare felicity in speedy reading of books," and preaching, early in his ministry, with a sternness that he mitigated in later years:He would pronounce the word damn with such an emphasis, as left a doleful echo in his auditors' ears a good while after... .

But in his older age he altered his voice and remitted much of his former rigidness; often professing that to preach mercy was that proper office of the ministers of the Gospel.

"[9] Perkins thus began a lifelong association with the "moderate-puritan" wing of the Church of England which held views similar to those of the continental Calvinist theologians Theodore Beza, Girolamo Zanchi, and Zacharias Ursinus.

[10] As a "moderate Puritan", Perkins was firmly opposed to non-conformists and other separatists who refused to conform to the Church of England.

[4] On 13 January 1587, Perkins preached a sermon denouncing the practice of kneeling to receive Communion, and was ultimately called before the Vice-Chancellor as a result.

Perkins was a proponent of "double predestination"[6][13] and was a major player in introducing the thought of Theodore Beza to England.

Writing less than a century after Perkins's death, his biographer Thomas Fuller recounted an objection that Perkins's views on double predestination often prompted:Some object that his doctrine, referring all to an absolute decree, hamstrings all industry, and cuts off the sinews of men's endeavours towards salvation.

For, ascribing all to the wind of God's Spirit, (which bloweth where it listeth,) he leaveth nothing to the oars of man's diligence, either to help or hinder to the attaining of happiness, but rather opens a wide door to licentious security.

[6] James Montagu preached his funeral sermon, taking as his text Joshua 1.2, ‘Moses my servant is dead’.