It may have been his marriage which brought Parry into the circle of the Princess Elizabeth, for the Forteccue family manor of Ponsbourne Park is only seven miles east of Bishop's Hatfield where she was kept in custody for most of her youth. He was appointed her cofferer (or business manager), but it is not known when, possibly while she was living with the Admiral of the Fleet, Lord Seymour and his wife, Queen Catherine Parr in Chelsea (Middlesex) and Sudeley Castle (Gloucestershire). Living with her step-mother, Elizabeth had few expenses and Parry was able to amass a large cash surplus for her from the lands she inherited from Henry VIII. He managed these too and added to them significantly, purchasing prominent manors like Ewelme in Oxfordshire, not far from his own Wallingford home.

When Seymour was arrested in January 1549, Thomas was taken to the Tower along with the Princess's Governess. Queen Catherine having died, it was suspected that Lord Seymour had recruited him as an ally in his scheme to persuade Princess Elizabeth to marry him, for Thomas was known to be one of her favourite attendants. However, Thomas only ever confessed to having talked about marriage in general with the princess. Although, he did admit to the Admiral having taken a particular interest in her landed inheritance, especially the possibility of their pooling resources; and he had also discovered from the Governess why they had all had to leave the Seymour household the previous year. For the Admiral had been caught red-handed, by his wife, with Princess Elizabeth in his arms. This was later confirmed by the governess, who was considerably put out by Thomas indiscretion. There was, apparently, no plot, but Thomas' testimony was enough to seal Lord Seymour's fate. He was executed for treason.

Parry's loose tongue seems to have done his reputation little harm with the Princess (or the Government) and, by September, he was part of her household once more, residing at the old Bishop's Palace at Hatfield in Hertfordshire. In 1551 and 2, some £4,600 (£1m today) were passing through Thomas' hands, from which he was able to pay expenses for both years and still be left with £1,500 (£300,000 today) for the Princess' coffers. It was around this time that Parry began corresponding with his fellow Welshman, William Cecil, secretary to the the Lord Prortector of the Realm (and Admiral Seymour's brother), the Duke of Somerset. Cecil was to become the great Elizabethan statesman, Lord Burghley, and it is possible that he owed his magnificent career to Parry. For he appears to have been the first to recommend Cecil to the Princess Elizabeth who, the following year, appointed him as her surveyor.

During the troubled times of her sister, Mary Tudor's reign as queen, Thomas showed his extreme loyalty to Princess Elizabeth. In March 1554, after Sir Thomas Wyatt's Rebellion, she was sent to the Tower of London, the Royal Council being worried by her earlier decision to move her household within the fortifications of Donnington Castle in Berkshire (although this never actually happened). Fortunately, her incarceration only lasted two months and she was, instead sent to Woodstock Palace where she was kept under the close supervision of Sir Henry Bedingfield. Three days after her arrival, the Council decided that there was no need for them to provide accommodation for her cofferer who could provide money for her household from London or anywhere else. Bedingfield therefore sent Parry packing. However, Thomas did not go very far. Much to Bedingfield's consternation, he took lodgings in the town where he made it his mission to make the life of the Princess' gaoler a misery. First, he protested that the Princess should not be paying for Bedingfield's official retinue. So a warrant was issued ordering the gaoler to pay for them himself. Bedingfield disliked the pair, but could prove nothing treasonable against either the Princess or Parry. He believed books that Parry was sending to his charge were seditious, but the only ones he intercepted were harmless. He felt he had become a helpless irrelevance. It was Parry who ran the show, with up to forty of his personal servants, as well as the princess's, calling on him daily at the Bull Inn in Woodstock for instructions. Eventually, the Royal Council forbade such large gatherings, but they did not curtail his actions further for the fear of a public outcry. All was well again by October 1555, when Elizabeth was allowed to take possession of her estates and so returned to Bishop's Hatfield, along with Thomas. He sat in Parliament for Wallingford again that year and even kept his head down by not opposing government bills. He was too busy stockpiling weapons and gathering support for Elizabeth as Queen Mary's health deteriorated. Three years later, he was appointed Lord Lieutenant of Berkshire, but, in Parliament, sat for Hertfordshire instead.

On 17th November 1558, Queen Mary died and Princess Elizabeth succeeded, peacefully, to the Throne as Queen Elizabeth I. She immediately rewarded Thomas' services with a knighthood, a seat on her Privy Council and the appointment of Controller of her Household. At the time, he was described by the Spanish Ambassador, Feria, to King Philip II, as "a fat man whom your majesty will have seen at Hampton Court". He considered him the most moderate member of the Royal Council. Thomas was also made Master of the Court of Wards and Liveries the following April.

Parry is said to have been the chief promoter of Lord Dudley's proposed marriage with the Queen and, to him, Sir Nicholas Throckmorton, the Ambassador to France, addressed, in November 1560, a vigorous remonstrance on the subject. After reading it, Sir Thomas was not "over-courteous" to the secretary, Jones, who brought it, though he appeared "half ashamed of his doings".

In the year of his death, the Queen presented Sir Thomas with the manor of Hamstead Marshall, not far from Welford. Some say it was here that, years before, Princess Elizabeth had given birth to Lord Seymour's child. Sir Thomas died on 15th December 1560 of "mere ill-humour," at the outcome of the Dudley affair, according to popular report, and was buried in Westminster Abbey. He left two sons and two daughters. His heir was his eldest son, Sir Thomas Parry Junior (1544-1616). Lady Parry, who was one of the ladies of the Privy Chamber, was granted, about 1566, an annuity of £50 for thirty-three years. She died on 5th January 1585 and was buried in Welford Church, where a fine wall monument to her memory still exists.