He also fought in the St James's Day Battle, as captain of the 48-gun Bristol.

In 1670-1 he was in Vice Admiral Sir Edward Spragge's expedition against the corsairs of Algiers.

He commanded the Gloucester (62 guns) in the attack on the Dutch Smyrna fleet in 1672, which opened the Third Anglo-Dutch War, capturing one of the Dutch ships though it sank almost immediately because of damage inflicted in the fight.

In 1673 he was promoted to flag rank, and in 1677–1679 was Commander-in-Chief of the fleet in the English Channel.

In 1675, Sir John was appointed Governor of Hurst Castle, and from 1677 to 1685 was Member of Parliament for Newtown, Isle of Wight.