Godolphin served under his brother, Sidney, at the Treasury, and was elected alongside Sidney as an MP for Helston in 1681. He attended the Oxford Parliament, but played no known part in it. After the dissolution of parliament, he was given a post in the stannary administration in Cornwall, which he held until his death. Godolphin was re-elected for Helston in 1685, but was again inactive in the Commons. He was elected to the Convention Parliament in 1689, during which he was appointed to eight committees and made 15 recorded speeches.[1]
He was soon identified with Tory politics; he voted to agree with the Lords that the throne was not vacant after the flight of James II, and supported the includsion of the phrase "to preserve the Church, as it is now established by law" in the new Coronation Oath Act 1688.[1] Godolphin was appointed to a committee tasked with thanking the King for his declaration to maintain the Church of England. He proposed an amendment to the Bill of Rights 1689, asserting the merit of Mary II's right to the throne so that "the monarchy might be looked upon as hereditary and not elective".[1] He defended the amendments against criticisms that it served French interests. He opposed the bill to suspend of the Habeas Corpus Act 1679, declaring that "some time ago we did arraign the Government of arbitrary power exercised against law. We go about now to establish arbitrary government by law".[1]
He continued to support his brother, Sidney, throughout his leadership of the ministry. Godolphin gave up his parliamentary seat at the second election of 1701 when it was declared incompatible with his position as chairman of the Board of Customs.[1] He was a justice of the peace for Cornwall by 1701. In 1702, he was appointed a commissioner to negotiate union with Scotland. He, and other Tory commissioners, duly convened at Whitehall Palace in November 1702, but the group showed little interest in progressing the issue. The commission was adjourned on 3 February 1703 until October, but never reconvened.[2]