In the reign of King James II. Mr. Baxter was committed to the King's Bench prison by warrant from the Lord Chief Justice Jefferies, for his "Paraphrase on the New Testament," which was called a scandalous and seditious book against the government. On May 30, 1685, he was brought to his trial. The passages mentioned in the information, were his paraphrase on Matt. v. 19; Mark ix. 39; xi. 31; xii. 38-40; Luke x. 2; John xi. 57; Acts xv. 2: and a certain noted clergyman put into the hands of his enemies some accusations out of his paraphrase on Rom. xiii. &c. as against the king, to touch his life; but no use was made of them. Jefferies interrupted his council in pleading for him, and treated Mr. Baxter most scornfully and rudely. He had given judgment against him, June 29, when he was fined 500 marks, and to lie in prison till he paid it; and bound to his good behaviour for seven years. But the next year King James altering his measures, many of the dissenters that were imprisoned were released; and their fines were remitted: and among the rest, Mr. Baxter obtained his pardon by the mediation of the Lord Powis. His fine was remitted; and Nov. 24, Sir Samuel Astrey sent his warrant to the keeper of the King's Bench to discharge him. But he gave sureties for his good behaviour: his Majesty declaring for his satisfaction, that it should not in him be interpreted a breach of the good behaviour for him to reside in London, which was not allowable by the Oxford Act; and this was entered upon his bail-piece. He continued some time in the Rules; and in February following removed to a house in Charter-house Yard.
After his settlement there, he gave Mr. Sylvester (whom he peculiarly valued, and had a special intimacy with) and his flock, his pains, gratis, every Lord's day in the morning, and every other Thursday morning at a weekly lecture. And thus he continued for about four years and a half; rejoicing as much as any man at the happy revolution under the conduct of King William, though he appeared not much in public. And when he was quite disabled from public service by his growing weakness, he still continued to do good in his own hired house, where he opened his doors morning and evening every day, to all that would come to join with him in family worship; reading and expounding the Scriptures with great seriousness and freedom. At length his distempers took him off from this also, and confined him first to his chamber, and then to his bed. Under sharp pains, he was very submissive to the will of God; and when he was inclined to pray most earnestly for a release, he would check himself and say, "It is not fit for me to prescribe: Lord, when thou wilt, what thou wilt, how thou wilt." As his end drew near, being often asked by his friends, how it was with his inward man, he replied, "I bless God I have a well-grounded assurance of my eternal happiness, and great peace and comfort within." He gave excellent counsel to young ministers that visited him, earnestly prayed God to bless their labours, and expressed great hopes that God would do a great deal of good by them, and great joy that they were of moderate and peaceable spirits. Being at last asked how he did, his answer was, "Almost well;" and at length he expired, Dec. 8, 1691, and was a few days after interred in Christ Church, in London, whither his corpse was attended by a numerous company of persons of different ranks, and especially of ministers, some of them conformists, who paid him the last office of respect. There were two discourses made upon occasion of his funeral, one by Dr. Bates, and the other by Mr. Sylvester, which are both in print: the former may be met with in the Doctor's Works; and the latter at the end of Mr. Baxter's Life in folio.