The committee did not proceed to a new election until 19 May 1656, when George Gifford was chosen, but Horton obtained a new dispensation from Cromwell, and remained in possession until the Restoration.
On 5 November in that year he preached at St. Paul's Cathedral before the lord mayor and court of aldermen, and his sermon was printed.
[2] At the Restoration (England), on 2 August 1660 he was removed from the presidency of Queens' College, Cambridge, to make room for Edward Martin, who had been ejected in 1644.
When the Savoy Conference was appointed, Horton was nominated an assistant on the side of the Presbyterians, though, according to Richard Baxter, he never joined in the deliberations.
He was one of the divines who were silenced by the Bartholomew Act in 1662, but he conformed soon afterwards, On 13 June 1666 he was admitted to the rectorship of Great St. Helen's in Bishopsgate Street, London, and held it until his death.
[2] His biographer, John Wallis, who had been under his tuition at Cambridge, says he was "a pious and learned man, an hard student, a sound divine, a good textuary, very well skilled in the oriental languages, very well accomplished for the work of the ministry, and very conscientious in the discharge of it".
[2] He and Dillingham prepared for press a treatise written by Dr. John Arrowsmith entitled Armilla Catechetica, Cambridge, 1659, 4to.