After the ruling African Party for the Independence of Cape Verde (PAICV) decided to institute multiparty democracy in February 1990, Pires replaced president Aristides Pereira as general secretary of PAICV in August 1990. The PAICV lost the multiparty parliamentary and presidential elections held in early 1991 and was left in opposition. At a party congress in August 1993, Pires was replaced as general secretary by Aristides Lima and was instead elected as president of PAICV.
As a candidate for the party presidency at PAICV's September 1997 congress, he faced Jos Maria Neves and prevailed with 68% of the vote. He stepped down as PAICV president in 2000 in preparation for a presidential bid in the next year's election and he was succeeded by Neves. He officially announced his candidacy for the presidency of Cape Verde on September 5, 2000. Pires was the PAICV candidate in the February 2001 presidential election, defeating former prime minister Carlos Veiga of the Movement for Democracy (MpD) in the second round by just 17 votes. Pires took office on March 22; the MpD boycotted his inauguration, saying that the election was marred by a "non-transparent process". As president, Pires appointed Neves as prime minister. He ran for a second term in the presidential election held on February 12, 2006 and again prevailed over Veiga, this time winning in the first round by a 51 percent-49 percent margin.
