He assisted in the expulsion of Barebone's Parliament in 1653 and took an active part in the suppression of Penruddock's rising in the west country of July 1655. In October 1655 during the Rule of the Major-Generals he was appointed major-general for Berkshire, Sussex and Hampshire. Meanwhile, he had been elected member for Yarmouth in Norfolk in the parliament of 1654 and for Hampshire in that of 1656. He encouraged the Hampshire justices of the peace to suppress unlicensed alehouses in their county, and attempted to curtail the evangelising activities of itinerant Quaker preachers, towards whom he was extremely hostile. He supported the proposal to bestow a royal title upon Oliver Cromwell, who greatly esteemed him, and was included in the newly constituted Upper House. He obtained Lambert's place as major-general of the Foot and was even thought of as a fit successor to Oliver Cromwell.

As a member of the committee of nine appointed in June 1658 on public affairs, he was witness to the Protector's appointment of Richard Cromwell as his successor. He supported the latter during his brief tenure of power and his fall involved his own loss of influence. In November 1659 he took part in the futile mission sent by the offices of the London cabal of the New Model Army to General George Monck, the English military governor of Scotland.