In the November 2008 legislative election, in which PAIGC won a parliamentary majority, Pereira was elected to the National People's Assembly as a PAIGC candidate in the 28th constituency, located in Bissau, the capital.[3] He was chosen by PAIGC to replace Francisco Benante (also a PAIGC member) as President of the National People's Assembly after the election, and accordingly, on 22 December 2008 he was elected as President of the National People's Assembly. He received 60 votes, while a rival PAIGC candidate, Helder Proença, received 37.[4]
Presidency
Following the assassination of President João Bernardo Vieira by the army on 2 March 2009, the army stated that Pereira, as President of the National People's Assembly, would succeed Vieira as President of Guinea-Bissau on an interim basis, in accordance with the constitution.[5]
Pereira was sworn in on 3 March 2009;[6] according to the constitution, he had 60 days to organize a presidential election.[7] Prime Minister Carlos Gomes Junior and an Economic Community of West African States (ECOWAS) delegation were present for his swearing in. On that occasion, Pereira urged the international community to help Guinea-Bissau "regain the reflexes of a stable state".[8] The opposition Social Renovation Party (PRS) criticized Pereira's succession, arguing that "a debate open to all active forces in the country in an appropriate forum like parliament to reflect on the kind of state to set up" would have been preferable.[9] At Vieira's funeral on 10 March, Pereira said that meeting the 60-day deadline for holding a new election was "one of our greatest challenges."[10]
Pereira sought the PAIGC nomination for the presidential election, but on 25 April 2009, the PAIGC Central Committee chose Malam Bacai Sanhá, who was interim President of Guinea-Bissau from 1999 to 2000, as the party's presidential candidate. He received 144 votes, while Pereira received 118.[11][12] Sanhá went on to win the election and succeeded Pereira on 8 September 2009.[13]
On 12 April 2012, Pereira was ousted in a coup and succeeded by Mamadu Ture Kuruma, Chairman of the Military Command of Guinea-Bissau. Pereira and Prime Minister Carlos Gomes Júnior were arrested by the military as gunfire ensued in the capital of Bissau. The Chairperson of the African Union Jean Ping issued a statement rejecting the coup and demanded the release of Pereira and Gomes. The United Nations Security Council issued a statement saying that they "strongly condemn the forcible seizure of power".[14]
On 27 April 2012, the deposed leaders were freed and sent to the Ivory Coast.[15]