When Ireland became disturbed in 1689, Mr Leslie removed with his family to England, where he employed himself in writing political pamphlets to serve the cause which he had embraced; but, though opposed to the existing government he continued a zealous and active supporter of the church of England. About this time he entered into a controversy with the quakers, which is said to have arisen from the circumstance of his lodging with a family of that persuasion. This family he converted. The first of the several treatises which he wrote against the quakers is entitled, "The Snake in the Grass." It appeared in 1696, and soon ran into a second edition. It was answered by George Whithead in a pamphlet entitled, "An Antidote to the Snake in the Grass." In his second edition Mr Leslie noticed this answer; but he was again assailed in a production called, "Satan dissolved from his Disguises of Light," which also appeared in 1696. To this, and several other attacks, Mr Leslie replied at great length in "A Defence of a book entitled the Snake in the Grass." This again provoked a host of answers, amongst which was one by the quakers, entitled "A Switch for the Snake." To this Mr Leslie again replied in "A Second Defence, or the third and last part of the Snake in the Grass."

The most celebrated works of Mr Leslie, though these just enumerated discovered singular ability, were those which he wrote against the deists. The first of these was published, in 1697, in a letter to a friend, and was entitled "A Short and easy Method with the Deists." The friend alluded to in the title was a lady, though the work bears that it was a gentleman. Having been thrown accidentally into the company of infidels, she applied to Mr Leslie for "some short topic of reason, without running to authorities and the intricate mazes of learning." The treatise was effectual, and Mr Leslie, although it was not his original intention, was prevailed upon to publish it. This work he enlarged considerably in a second edition. No answer appeared to the Short and Easy Method till 1710, when it was replied to in a treatise entitled "A detection of the true meaning and wicked designs of a book entitled," &c. Mr Leslie replied to this attack in "The Truth of Christianity Demonstrated," to which was prefixed, "A Vindication of the Short Method with the Deists." These works against deism produced a powerful effect, and amongst others the conversion of a person of the name of Gildon, who had acquired considerable celebrity as a member of that persuasion. This man not only professed himself convinced of his errors, and publicly retracted them, but wrote a book against the opinions which he had formerly entertained, entitled "The Deist’s Manual, or a rational Inquiry into the Christian Religion."

Encouraged by the success of his attack on deism, Mr Leslie, in 1699, produced his "Short Method with the Jews," a work which was first suggested by a similar circumstance with that which had given rise to his Short Method with the Deists. An eminent Jew had been converted by his reasoning, and had intimated his intention of publicly owning his conviction. The convert, however, died during Mr Leslie’s absence, without exhibiting the recantation which he had proposed.

The next controversy in which Mr Leslie was engaged, was with the Socinians. It began in 1694. In 1697 he published the first of the six dialogues, entitled "The Socinian Controversy Discussed." This was answered in a short tract, entitled "Remarks on Mr Charles Leslie’s First Dialogue on the Socinian Controversy." Mr Leslie replied, and was again answered by his opponent in "A Vindication of the Remarks." Mr Leslie now published "A Reply to the Vindication," and with this ended the first part of the controversy.

His principal works against the papists were, "The True Nature of the Catholic Church, in answer to the Bishop of Meaux’s letter to Mr Nelson," printed in 1703; "The Case Stated between the Church of Rome, and the Church of England, published in 1713; and "Of Private Judgment and Authority in Matters of Faith." These works are said to have made several converts from popery.

Although thus earnestly and laboriously employed in the cause of religion, Mr Leslie did not neglect the interests, so far as any efforts of his could serve them, of the exiled family. He wrote several political tracts during this period, and made several journeys to Bar le Duc to visit the Pretender, who was then residing there. These journeys, however, and his political treatises, especially one, entitled "The Good Old Cause," published in 1710, gave such offence to the ruling party, that it is said a warrant for his apprehension was actually issued against him. However this may be, he found it necessary to quit the kingdom in 1713, when he proceeded to Bar le Duc, and took up his residence by invitation with the Pretender, who procured a room to be fitted up for him in his own house. While here, Mr Leslie was permitted to officiate in a private chapel after the manner of the church of England, and it is even said, that the Pretender had promised to listen to his arguments concerning his religion, and that Mr Leslie had in vain endeavoured his conversion. This, however, is contradicted by lord Bolingbroke, who asserts, that he not only refused to listen to Mr Leslie, but forbade all discussion on religious matters. Notwithstanding of this, however, and of several other subjects of dissatisfaction with the chevalier, whose conduct towards him does not appear to have been altogether adjusted to his deserts, Mr Leslie continued to remain with him, and in 1716 accompanied him into Italy, after his unsuccessful attempt upon England. Here he remained till 1721, when he found his situation so exceedingly disagreeable, that he determined on returning to his native country. This he accomplished, but died in the following year, on the 13th April, in his own house, at Glaslough, in the county of Monaghan.