In 1998 he was elected Governor of Adamawa State. While still Governor-Elect he was selected by the Peoples Democratic Party (PDP) Presidential candidate Olusegun Obasanjo as his running mate. The duo went on to win elections in February 1999, and Abubakar was sworn-in as Nigeria’s second democratically elected vice president on 29 May 1999.
Abubakar’s second term as Vice President was marked by a stormy relationship with President Obasanjo. His bid to succeed Obasanjo did not receive the latter’s support, and it took a judgment of the Supreme Court to allow Abubakar contest after he was initially disqualified by the Independent National Electoral Commission on the grounds that he had been indicted for financial misconduct by an investigating panel set up at Obasanjo’s behest. The Supreme Court ordered the electoral commission to restore Abubakar’s name onto the presidential ballot. Abubakar ran on the platform of the Action Congress, having quit the PDP on account of his issues with President Obasanjo. Abubakar lost the election, placing third after Umaru Yar’Adua and Muhammadu Buhari of the All Nigeria Peoples Party (ANPP).