The sequence of events that led to Somerset's removal from power has often been called a coup d'état. By 1 October 1549, Somerset had been alerted that his rule faced a serious threat. He issued a proclamation calling for assistance, took possession of the king's person, and withdrew for safety to the fortified Windsor Castle, where Edward wrote, "Me thinks I am in prison". Meanwhile, a united Council published details of Somerset's government mismanagement. They made clear that the Protector's power came from them, not from Henry VIII's will. On 11 October, the Council had Somerset arrested and brought the king to Richmond. Edward summarised the charges against Somerset in his Chronicle: "ambition, vainglory, entering into rash wars in mine youth, negligent looking on Newhaven, enriching himself of my treasure, following his own opinion, and doing all by his own authority, etc." In February 1550, John Dudley, Earl of Warwick, emerged as the leader of the Council and, in effect, as Somerset's successor. Although Somerset was released from the Tower and restored to the Council, he was executed for felony in January 1552 after scheming to overthrow Dudley's regime. Edward noted his uncle's death in his Chronicle: "the duke of Somerset had his head cut off upon Tower Hill between eight and nine o'clock in the morning".
The Earl of Warwick's rival for leadership of the new regime was Thomas Wriothesley, 1st Earl of Southampton, whose conservative supporters had allied with Dudley's followers to create a unanimous Council, which they, and observers such as the Holy Roman Emperor Charles V's ambassador, expected to reverse Somerset's policy of religious reform. Warwick, on the other hand, pinned his hopes on the king's strong Protestantism and, claiming that Edward was old enough to rule in person, moved himself and his people closer to the king, taking control of the Privy Chamber. Paget, accepting a barony, joined Warwick when he realised that a conservative policy would not bring the emperor onto the English side over Boulogne. Southampton prepared a case for executing Somerset, aiming to discredit Warwick through Somerset's statements that he had done all with Warwick's co-operation. As a counter-move, Warwick convinced parliament to free Somerset, which it did on 14 January 1550. Warwick then had Southampton and his followers purged from the Council after winning the support of Council members in return for titles, and was made Lord President of the Council and great master of the king's household. Although not called a Protector, he was now clearly the head of the government.
Warwick's war policies were more pragmatic than Somerset's, and they have earned him criticism for weakness. In 1550, he signed a peace treaty with France that agreed to withdrawal from Boulogne and recalled all English garrisons from Scotland. In 1551, Edward was betrothed to Elisabeth of Valois, King Henry II's daughter, and was made a Knight of Saint Michael. In practice, he realised that England could no longer support the cost of wars. At home, he took measures to police local unrest. To forestall future rebellions, he kept permanent representatives of the crown in the localities, including lords lieutenant, who commanded military forces and reported back to central government.