On 13 April 1636 he was installed by Bishop John Williams prebendary of Layton Ecclesia in Lincoln Cathedral, just vacated by the death of his friend George Herbert.
In 1641 he published at the University Press his first tractate, Of the Government of Churches: a Discourse pointing at the Primitive Form, and in the following year Of Religious Assemblies, and the Publick Service of God.
In 1644 the disfavour into which Trinity College had fallen with the parliamentary party compelled Thorndike to retire from his living of Barley, which was sequestered to Henry Prime, a parishioner; in 1647 one Peter Smith was appointed minister, on whose death (August 1657) Nathanael Ball succeeded.
In July 1660 he published his Due Way of composing Differences, and on 20 March 1661 was appointed to assist at the Savoy Conference, where he took a minor part but suffered a barb from Richard Baxter.
In June 1667 he again returned to Trinity, but his acceptance a few weeks later of the tithes of Trumpington parish involved the surrender of his fellowship, and he accordingly retired to his canonry at Westminster, where he took up residence in the cloisters.
The year 1670 saw the appearance of his Discourse of the Forbearance or Penalties which a due Reformation requires, and also of the first part of his De Ratione ac Jure finiendi Controversias Ecclesiae Disputatio, the restating the argument of the Epilogue and other works.
Thorndike's position as a theologian was unusual and some of his views were challenged from his own side of the debates, in particular by Isaac Barrow in his posthumous tract on The Unity of the Church, and by Henry More in his Antidote to Idolatry.
He countenanced the practice of prayers for the dead; and by Cardinal Newman he was regarded as the only writer of any authority in the English church who held the true theory of the Eucharist.