Parliament held Charles under house arrest at Holdenby House in Northamptonshire until Cornet George Joyce took him by threat of force from Holdenby on 3 June in the name of the New Model Army. By this time, mutual suspicion had developed between Parliament, which favoured army disbandment and presbyterianism, and the New Model Army, which was primarily officered by congregationalist Independents, who sought a greater political role. Charles was eager to exploit the widening divisions, and apparently viewed Joyce's actions as an opportunity rather than a threat. He was taken first to Newmarket, at his own suggestion, and then transferred to Oatlands and subsequently Hampton Court, while more fruitless negotiations took place. By November, he determined that it would be in his best interests to escape—perhaps to France, Southern England or Berwick-upon-Tweed, near the Scottish border. He fled Hampton Court on 11 November, and from the shores of Southampton Water made contact with Colonel Robert Hammond, Parliamentary Governor of the Isle of Wight, whom he apparently believed to be sympathetic. But Hammond confined Charles in Carisbrooke Castle and informed Parliament that Charles was in his custody.

From Carisbrooke, Charles continued to try to bargain with the various parties. In direct contrast to his previous conflict with the Scottish Kirk, on 26 December 1647 he signed a secret treaty with the Scots. Under the agreement, called the "Engagement", the Scots undertook to invade England on Charles's behalf and restore him to the throne on condition that presbyterianism be established in England for three years.