At the same time he was urged to accept the deanery of Lichfield and Coventry, but like Richard Baxter, Edmund Calamy the elder, Thomas Manton, and others in their position, he declined office.
In 1665 Bates took the oath imposed by the parliament which met at Oxford 'that he would not at any time endeavour an alteration in the government of church or state.'
[2] In 1668 some of the more moderate churchmen endeavoured to work out a scheme of comprehension that would bring presbyterians back into the Church of England.
He successfully interceded with Archbishop Tillotson in behalf of Nathaniel, Lord Crewe, bishop of Durham, who had been excepted from the act of indemnity of 1690.
In the last years of his life he was pastor of the Presbyterian church of Hackney; he died there on 14 July 1699, aged 74, having outlived and preached the funeral sermons of Baxter, Manton, Thomas Jacomb, and David Clarkson.