Barlow wrote at the request of Robert Boyle an elaborate treatise on "Toleration in Matters of Religion" at this time, but it was not published until after his death (in "Cases of Conscience", 1692). Barlow's reasoning is based more on expediency than on principle. He shows that the religious toleration he advocates does not extend to atheists, papists or Quakers. Earlier, when Jews were applying to Cromwell for readmission into England, Barlow had composed "at the request of a person of quality" a tract on "Toleration of the Jews in a Christian State", published in the same collection. On the other hand, Barlow was one of a group of Oxford grandees hostile to the Royal Society, along with John Fell, Obadiah Walker, and Thomas Pierce. He was an enemy of the "new philosophy" (as propounded by leading Royal Society members), giving as his confessional reasons that it was "impious if not plainly atheistic, set on foot and carried on by the arts of Rome," so designing to ruin the Protestant faith by disabling men from defending the truth. He noted the Catholic background of Descartes, Gassendi, Mersenne and Du Hamel. His "Directions to a young Divine for his Study of Divinity" of this period contain a catalogue of theological works classified by subjects, with remarks on their value and character.