Baxter's health had grown even worse, yet this was the period of his greatest activity as a writer. He wrote 168 or so separate works, including major treatises such as the Christian Directory, the Methodus Theologiae Christianae, and the Catholic Theology. His Breviate of the Life of Mrs Margaret Baxter records the virtues of his wife and tenderness which otherwise might not have been known. A slim devotional work published in 1658 under the title Call to the Unconverted to Turn and Live formed one of the core extra-biblical texts of evangelicalism until at least the middle of the 19th century.

The remainder of his life, from 1687 onwards, was passed peacefully. He died in London and his funeral was attended by churchmen as well as dissenters.