The younger son of Queen Maria I, João de Bragança became heir to the Portuguese throne after the death of his older brother, and in 1799 took power as prince regent due to his mother's mental illness, a situation that lasted until Maria's death in 1816. João had married Carlota Joaquina, the eldest daughter of Charles IV of Spain, and supported his fight against the French republic. After the Franco-Hispanic peace treaty of Basel in 1795, however, Spain turned against its former Iberian ally and invaded Portugal briefly in 1801. Portugal's situation turned even more critical six years later, when Napoleon's armies crossed Spain and, in November, approached Lisbon, forcing the Royal Court into a hasty retreat to Salvador and, finally, Rio de Janeiro which, from January 1808, became the new capital of the Portuguese empire. Britain was to benefit the most from this new situation, as, in return for British support against the French invaders, João was forced to grant commercial privileges to British traders that turned Brazil into a de facto colony of the British empire (the maximum duty on British imports, for instance, was one percent below that on Portuguese goods!)

But João´s arrival in Guanabara bay also marked the beginning of a more aggressive politics of territorial expansion inland, following his declaration of a "holy war" (or "guerra justa", a legal figure which had not been employed since the Reconquista) against the Guarapuava Indians in 1809. Despite the clamor in the Portuguese motherland for the return of the monarch mounted following the expulsion of the French by a British army in 1808, and increasingly after Napoleon's surrender in 1814, João chose to remain in his tropical capital, where he had revoked all previous prohibitions on manufacturing, helped set up a naval and military academy in 1808 and 1810, inaugurated, in 1814, a library containing sixty thousand volumes, and, some years later, founded the French-staffed Academy of Fine Arts. When, after the death of his mother in 1816, João could finally ascend the throne in his own right, he did so as "King of the United Kingdoms of Portugal, Brazil, and the Algarves", thus raising the former colony to a judicially equal status with the Portuguese "mainland".

The Portuguese côrtes, however, a parliamentary body set up after the expulsion of the French, grew increasingly impatient over the monarch's reticence to return to Lisbon, and when, in 1820, the radical revolution in neighbouring Spain threatened to spread into Portugal, João finally sailed home, leaving his son Pedro I in Rio de Janeiro. Portugal's elite was split into a powerful radical faction that imposed a liberal constitution in 1820, but was finally overthrown -with the support of the French- in 1823, and an absolutist group gathering around Queen Carlota Joaquina and her son Miguel, who was made commander-in-chief after the restoration of royal authority in 1823. By 1822, however, Pedro had declared Brazil's independence at Ipiranga, on the outskirts of São Paulo, and João, attempting to steer a middle course between Portuguese, Brazilians, liberals, and absolutists, separated from his wife and sent Miguel into exile, reluctantly accepting Brazil's independence in 1825. He died in March of the following year in Lisbon -the city in which he was born but, presumably, would have preferred to continue avoiding-, leaving his daughter Maria Isabel as regent of Portugal. The problem of dynastic succession, however, was not solved until Pedro II´s abdication to the Portuguese throne in favour of his own daughter Maria da Glória, the future Queen Maria II.

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