He resigned his post in 1550 and on 23 May became a member of the Privy Council of Edward VI. After Edward's death, Brooke supported the attempt by John Dudley, 1st Duke of Northumberland to place his daughter-in-law Lady Jane Grey on the throne. He was pardoned by Queen Mary I, but subsequently fell under suspicion again. His nephew, Sir Thomas Wyatt the younger was the leader of Wyatt's Rebellion, a Protestant rebellion which brought suspicion on the whole family. Brooke's daughter, Elizabeth Brooke, is thought to have been the instigator of the plot to place Lady Jane Grey on the throne instead of Mary I. During his Rebellion, Wyatt besieged Lord Cobham in Cooling Castle and although Cobham claimed to have resisted, following the failure of the rebellion he was accused of complicity in it and was imprisoned in the Tower of London for a brief period. The next year, at the start of the Roman Catholic Queen's formal reconciliation with the Holy See, he was assigned to welcome to England the papal legate Cardinal Pole, who went on to be responsible for many Protestant martyrdoms in England. The entertainment is recorded as having taken place at Cooling Castle in 1555. Thereafter Cobham limited himself to local affairs in Kent.