A few hours before embarking for Brazil, on 27 November 1807, D. Joao issued a declaration to his ‘faithful and beloved subjects’, explaining the reasons for his departure and announcing the appointment of a council of regency. The council was to prove totally ineffective, not least because D. Joao had expressly forbidden it from resisting the French invaders. Unlike Spain, however, Portugal had preserved its monarchy and hence Napoleon could not claim the Portuguese crown for himself or for one of his brothers. While Carlos IV and his son Fernando VII resigned the Spanish throne into Napoleon's hands during their confinement in France in 1808, the House of Braganca never renounced its rights. Although Junot declared the authority of House of Braganca extinguished on 5 February 1808, this unilateral proclamation was unlikely to be recognized by other European powers.

For a while it seemed that the French would encounter little opposition in either Spain or Portugal. But, as Holland had always appreciated, the peoples of the Peninsula were fiercely independent; the real question was whether, in the event of a rising, leaders of sufficient quality would emerge or foreign powers, especially Britain, would provide effective support. Madrid was the first town to rise on 2 May 1808. Although the rebellion was quickly suppressed and ended with the execution of at least one hundred people, it encouraged risings elsewhere. Within two months, patriotic juntas had been established throughout the Peninsula. Influenced by developments in Galicia, the first Portuguese risings broke out in the north, in Chaves and Oporto, on 6 June 1808. The first Oporto rising collapsed after three days owing to the cowardice of the military governor, Brigadier Luis Osorio. Two weeks later, however, on 18 June, a new rebellion led to the establishment of a patriotic junta headed by the bishop of Oporto. There were further risings, at Leiria on 30 June and Evora on 20 July, though both were suppressed. Most crucially, however, the remaining French troops left Lisbon on 15 September, though with British protection and under the terms of the controversial Anglo- French Convention of Sintra (30 August 1808).