Henry II inherited Woodstock from his grandfather Henry I, expanded it, and made it his favored country residence. He kept his mistress Rosamund Clifford here - 'Fair Rosamund' of the medieval legend, said to be lodged in a bower at the heart of a maze that only Henry could navigate. Whether the maze was real or a later embellishment, Rosamund was. She died around 1176 and was buried at Godstow Nunnery just outside Oxford. The English royal habit of fathering children at Woodstock did not stop with Henry II. The palace eventually became the birthplace of multiple royal children: Edmund of Woodstock, sixth son of Edward I, in 1301. Edward the Black Prince, heir to Edward III and one of the most famous English warriors of the Hundred Years' War, in 1330. Isabella, eldest daughter of Edward III, in 1332. Thomas of Woodstock, Duke of Gloucester, in 1355. The palace, when full of court, was effectively a royal nursery.

Woodstock was the setting for some of the major diplomatic events of medieval and early-modern Britain. King William the Lion of Scotland married Ermengarde de Beaumont here in 1186. In 1247, Henry III signed the Treaty of Woodstock with Llywelyn ap Gruffudd, the Welsh prince who was Llywelyn the Great's grandson - a treaty that briefly secured peace before war returned. In 1361, Mary of Waltham, daughter of Edward III, was married here to John IV, Duke of Brittany. On Palm Sunday 1501, the poet laureate John Skelton is said to have staged his play Nigramansir - The Necromancer - at the palace for Henry VII. The play is completely lost. No copy survives. Henry VII rebuilt much of Woodstock in the 1490s, spending over £4,000 from his personal chamber account on construction supervised by William Este of Oxford. The hall got a new roof in 1494, designed by the Oxford carpenter John Brian. Brian and the king's officials argued over the design and the cost. Some things about royal building projects never change.

On 15 August 1497, a betrothal ceremony was held at Woodstock for Catherine of Aragon and Prince Arthur, eldest son and heir of Henry VII. Catherine was eleven and still in Spain. Arthur was eleven and at Woodstock. The marriage took place by proxy. Arthur would die five years later, in 1502, leaving his younger brother - the future Henry VIII - to marry his widow, a transaction that would eventually lead to the English Reformation. Henry VIII himself visited Woodstock in August 1532. He played dice and gave money to a man described in the household accounts as 'frantic.' According to William Latymer, Anne Boleyn while at Woodstock was kind to one of her gentlewomen, Mrs Jaskyne, allowing her to leave court to visit her sick husband. Such small gestures were noted because Anne, two years later, would be executed for treason and Henry would burn most of her papers.

From 20 May 1554 until June 1555, the future Queen Elizabeth I was held at Woodstock as a prisoner of her half-sister, Queen Mary I. Elizabeth was suspected of involvement in Wyatt's Rebellion. Her keeper was Sir Henry Bedingfield, a careful Catholic gentleman who refused to allow her the cloth of estate that signified royal status, and who insisted on five or six locked doors between her lodging and the garden. The chronicler John Foxe records that Elizabeth could hear milkmaids singing in the garden and envied them their freedom. While imprisoned in the gatehouse, Elizabeth scratched verses on the palace windows with a diamond ring. One of them was: 'Much suspected by me, / Nothing proved can be, / Quoth ELIZABETH the prisoner.' Mary, Queen of Scots, would quote this couplet in 1584, by which time Elizabeth was queen and Mary was the prisoner. Travelers in 1600 still made special trips to see the scratched window. The room where Elizabeth had slept was preserved and called Queen Elizabeth's Chamber for the next two hundred years.

King James I and Anne of Denmark visited Woodstock in September 1603 during an outbreak of plague in London. Sir Robert Cecil was unimpressed by the building. 'Unwholesome,' he wrote, 'all the house standing upon springs. It is unsavoury, for there is no savour but of cows and pigs. It is uneaseful.' The palace had been deteriorating for a century. The Civil War finished it. Royalist troops occupied Woodstock during the war; Parliamentary forces took the palace and demolished most of it after the conflict. The 1649 survey describes a large gatehouse, a great hall, a chapel, the Bishop's Lodgings, the Queen's Hall, and a presence chamber - most of it empty of furniture, all of it about to be torn down. In 1705, Parliament granted the manor and honour of Woodstock to John Churchill, 1st Duke of Marlborough, in reward for his victory at the Battle of Blenheim the previous August. Marlborough built Blenheim Palace on the manor as his seat. Some of the stone came from the old palace ruins. The Duke holds the manor by feudal tenure that requires him to present a standard with the fleur-de-lis of France at Windsor Castle every 13 August - the anniversary of Blenheim - in perpetuity. The current Duke still pays the rent.