Concerned that Britain might intervene in Portugal, an old and important ally, or that the Portuguese might resist, Napoleon decided to speed up the invasion timetable, and instructed Junot to move west from Alcántara along the Tagus valley to Portugal, a distance of only 120 miles (193 km). On 19 November 1807, Junot set out for Lisbon and occupied it on 30 November.

The Prince Regent John escaped, loading his family, courtiers, state papers and treasure aboard the fleet, protected by the British, and fled to Brazil. He was joined in flight by many nobles, merchants and others. With 15 warships and more than 20 transports, the fleet of refugees weighed anchor on 29 November and set sail for the colony of Brazil. The flight had been so chaotic that 14 carts loaded with treasure were left behind on the docks.

As one of Junot's first acts, the property of those who had fled to Brazil was sequestered and a 100-million-franc indemnity imposed. The army formed into a Portuguese Legion, and went to northern Germany to perform garrison duty. Junot did his best to calm the situation by trying to keep his troops under control. While the Portuguese authorities were generally subservient toward their French occupiers, the ordinary Portuguese were angry, and the harsh taxes caused bitter resentment among the population. By January 1808, there were executions of persons who resisted the exactions of the French. The situation was dangerous, but it would need a trigger from outside to transform unrest into revolt.