Pedro I encountered a number of crises during his reign as Emperor of Brazil. A secessionist rebellion in the Cisplatina Province in early 1825 and the subsequent attempt by the United Provinces of the Río de la Plata (later Argentina) to annex Cisplatina led the Empire into the Cisplatine War: "a long, inglorious, and ultimately futile war in the south". In March 1826, John VI died and Pedro I inherited the Portuguese crown, briefly becoming King Pedro IV of Portugal before abdicating in favor of his eldest daughter, Maria II. The situation worsened in 1828 when the war in the south ended with Brazil's loss of Cisplatina, which would become the independent republic of Uruguay. During the same year in Lisbon, Maria II's throne was usurped by Prince Miguel, Pedro I's younger brother.

Other difficulties arose when the Empire's parliament, the General Assembly, opened in 1826. Pedro I, along with a significant percentage of the legislature, argued for an independent judiciary, a popularly elected legislature and a government which would be led by the emperor who held broad executive powers and prerogatives. Others in parliament argued for a similar structure, only with a less influential role for the monarch and the legislative branch being dominant in policy and governance. The struggle over whether the government would be dominated by the emperor or by the parliament was carried over into debates from 1826 to 1831 on the establishment of the governmental and political structure. Unable to deal with the problems in both Brazil and Portugal simultaneously, the Emperor abdicated on behalf of his son, Pedro II, on 7 April 1831 and immediately sailed for Europe to restore his daughter to her throne.