In the first months of the Scottish Reformation Châtellerault continued to support Mary of Guise. He faced a Protestant army with the French commander at Cupar Muir in June 1559. He changed his allegiance in August 1559, joining the Protestant Lords of the Congregation to oppose the regency of Mary of Guise, and lost his French dukedom as a result. In order to discredit him with the English government a letter was forged by his enemies, in which Châtellerault declared his allegiance to Francis II of France, but the plot was exposed. On 27 February 1560 he agreed to the Treaty of Berwick with Elizabeth I, which placed Scotland under English protection.