He is recorded as having been appointed to command the 42-gun Advice during the period of the Commonwealth, and as having signed the declaration of confidence in the leadership of Oliver Cromwell on 22 April 1653, made by the admirals and captains of the fleet.

From Advice he was appointed to command the newly built Essex in December 1653, and was given a small squadron of warships to patrol in the North Sea.

Cannon fire from either Mary or Royal Charles then ignited the Eendracht's power magazine, which blew up, destroying the ship and killing Admiral Jacob van Wassenaer Obdam.

[1] He returned to Britain and was appointed admiral of the blue squadron in the royal fleet, taking part in the Four Days' Battle in June 1666, under the overall command of George Monck, 1st Duke of Albemarle.

In doing so Smith prevented Tromp from coming to the assistance of Michiel de Ruyter, whose force was severely mauled by the van of the English fleet.

[1][6] During the battle Tromp's flagship lost over a hundred men, and was nearly captured by Sir Edward Spragge, one of Smith's junior flag officers.

[1] Eventually King Charles II intervened to settle the matter, largely in Smith's favour, and he remained in the navy despite professional enmities.

He had become an important landowner during his time in the navy, buying Prior House in Hemingbrough, near Selby in 1662, and acquiring land in the area, including the manor of Osgodby in 1668.