As royal champion Lee took part in many tournaments and other court functions, and between 1569 and 1573 fought against the northern rebels and the Scots. He is probably best known as lieutenant of Woodstock, a position he gained through Sir Robert Dudley, Earl of Leicester. Elizabeth visited him there after the Kenilworth entertainment of 1575, and again in 1592. Lee quarrelled with George Whitton over their respective positions at Woodstock, and in 1581, following a lawsuit, Whitton was imprisoned for a short time. Lee used his position at Woodstock to gain parliamentary seats for his half-brother Richard, and his more distant relative John Lee. He was himself four times knight of the shire for Buckinghamshire. He is not known to have spoken in the House, but was appointed to committees on the subsidy (10 Feb. 1576, 25 Jan 1581), the seditious practices bill (1 Feb 1581), the bill against ‘slanderous libelling’ (3 Feb), and one to fortify the frontier with Scotland (25 Feb). On 4 Feb he was one of those given a general commission to inquire into the Arthur Hall privilege case.

Lee had considerable estates in Buckinghamshire and Oxfordshire. He lost as many as 3,000 sheep in the great storm of 1570, and was reported to be building ‘four goodly mansions’ in the county. By 1580 he was in financial difficulties and the Queen made him a loan. Typically for an Elizabethan enclosure commissioner he was himself in trouble for enclosure, in 1596. At court he appears as a peacemaker, attempting to reconcile George Talbot, 6th Earl of Shrewsbury with his son, and in 1598 trying to persuade Robert Devereaux, 2nd Earl of Essex to ask the Queen's forgiveness. ‘Your wrongs may be greater than you can well digest, but consider how great she is, and how willing to be conquered’. He continued in favour under James I, who in Sep 1603 dined with him at Ditchley, near Woodstock, and later the same year granted him a pension of £200 p.a. Lee died at Spelsbury 12 Feb 1611, aged 80. His last years were spent with his mistress, Anne Vavasour, sister of Thomas, with whom Lee had contended at the tilt as long ago as 1584, when Anne was a gentlewoman of the bedchamber to Queen Elizabeth. The Queen apparently approved of their liaison, as the couple entertained her at Ditchley House in Sep 1592. In 1605, Lee pensioned off Capt. John Finch, the husband who Anne had married BEF 1590; and left Anne an income of £700 per year in his will, some property, and instructions for their joint burial in the tomb he had had erected for them in Quarrendon, Buckinghamshire.