The Portuguese royal family was based in Lisbon before fleeing to Brazil in 1807. Lisbon was Portugal’s capital, the seat of the monarchy, and the location from which the court organized its escape during the Napoleonic invasion of Portugal.
The transfer was driven by the conflict between Napoleon’s France and Britain. Napoleon demanded that Portugal close its ports to British trade, but Portugal hesitated. French troops under General Junot invaded Portugal in late 1807, while a British-supported evacuation plan allowed Queen Maria I, Prince Regent John, the Braganza family, officials, servants, and other members of the court to leave.
The embarkation took place at Lisbon on 27 November, although bad weather delayed the fleet’s departure until 29 November. The court eventually reached Brazil, where it established a Portuguese government in Rio de Janeiro. This unusual move made Brazil the center of the Portuguese Empire and transformed its political importance.
Sintra, Coimbra, and Porto were Portuguese cities, but none was the royal court’s main seat immediately before the flight. Lisbon is therefore the single canonical answer.