He succeeded his father in 1613, inheriting estates which included the lease of the Scilly Isles.

As he was a Royalist, when the Civil War broke out, he returned to Cornwall, where he secured the Scilly Isles for the King and raised a regiment of which his brother, William, took command.

In consequence, he was disbarred from sitting in Parliament in January 1644, and his estates were sequestered.

However, after the capture of the King he negotiated an honourable capitulation of the Scilly Isles to Parliament, with the House of Commons voting "that Mr Godolphin, governor of Scilly, upon his surrender of that island, with all forts &c, should enjoy his estate and be free from arrest for any acts of war".

He was elected once more for Helston in the Convention Parliament of 1660, and following the Restoration he was knighted at Charles II's coronation.