On the eve of the Peninsular Wars, he was appointed governor and captain-general of the Azores on 24 March 1806. He disembarked in Angra, then regional capital of the Captaincy General of the Azores on 4 May 1806, taking-up his role on the 10 May. On his arrival Miguel António was confronted by a famine on the island of São Miguel, and later by French invasion of Portugal, resulting in the transfer of the Portuguese Court to Brazil. On Junot's invasion, Miguel severed ties with the continent, now in the possession of the French forces; he ignored orders from Lisbon, supported by the exiled Royal family. When Junot's forces were expelled, the English liberators entered the picture, functioning with Vice-Regal authority, maintaining a duality between the power in Lisbon and that in Rio de Janeiro, making the Captains-General dependent functionaries of the state.