In August 1547, Clinton was sent to Scotland with a fleet of twelve ships to support the Siege of St Andrews Castle and prevent a French intervention, but he arrived too late. He captured Broughty Castle on 24 September, refortified it with the aid of an Italian military engineer, and installed Andrew Dudley as its captain, leaving him three ships, the Mary Hamborough, the Barque Eger, and the Phoenix. Clinton commanded the English fleet during the invasion of Scotland by Edward Seymour and provided naval artillery support at the Battle of Pinkie on 15 September 1547. In August 1548 he sailed into the Firth of Forth and scattered French and Scottish ships near Leith. He then landed 500 men to burn the ships in the harbour of Burntisland and contemplated fortifying the harbour for English use. He was aboard the Great Barque.
Governor of Boulogne
Appointed as Governor of Boulogne in 1547, Clinton successfully defended the city against a French siege from 1549 to 1550. That same year, with Henry Manners, 2nd Earl of Rutland, he was appointed Lord Lieutenant of Lincolnshire and of Nottinghamshire and served as Lord High Admiral under King Edward VI from 1550 to 1553, and again in the reign of Queen Elizabeth from 1559 to his death in 1585. He was a Privy Counsellor from 1550 to 1553 and briefly served as an envoy to France in 1551. After appointment as Lord-Lieutenant of Lincolnshire in 1552, Clinton took part in the defeat of Wyatt's Rebellion in Kent in 1554. He was a commander of the expedition of William Herbert, 1st Earl of Pembroke to support the Spanish forces at the Battle of Saint Quentin in northern France on 10 August 1557, but arrived after the battle was largely won. Upon his return to England, Clinton took command of the English fleet, raided the French coast and in 1558 burnt the town of Le Conquet and the surrounding area.
With Ambrose Dudley, 3rd Earl of Warwick, Clinton was in joint command of a large army during the Northern Rebellion; however the army was still being assembled when the rebellion was defeated in January 1570. He was created Earl of Lincoln in 1572, and served as ambassador to France, during which time he undertook several commissions from Queen Elizabeth I until his death in London on 16 January 1585. In 1541-42 following the dissolution of the monasteries, Clinton and his wife, Ursula, were granted the lands of the earlier Aslackby Preceptory of the Knights Templar—later belonging to the Knights Hospitaller—at Aslackby in Lincolnshire.
Marriage and progeny
He married three times:
Firstly to Elizabeth Blount, Henry VIII's former mistress, by whom he produced three daughters:
*Lady Bridget Clinton, married Robert Dymoke, of Scrivelsby, Lincolnshire, c. 1556 and had ten children. He was a devout Catholic and was declared a martyr after his death.