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.