On 1 September 1990, Abubakar announced his Gongola State gubernatorial bid. A year later, before the elections could hold, Gongola State was broken up into two – Adamawa and Taraba States – by the Federal Government. Abubakar fell into the new Adamawa State. After the contest he won the SDP Primaries in November 1991, but was soon disqualified by the government from contesting the elections.
In 1993, Abubakar contested the SDP presidential primaries. The results after the first ballot of the primaries held in Jos was: Moshood Abiola with 3,617 votes, Baba Gana Kingibe with 3,255 votes and Abubakar with 2,066 votes. Abubakar and Kingibe considered joining forces combining 5,231 votes to challenge Abiola. However, after Shehu Yar'Adua asked Atiku Abubakar to withdraw from the campaign, with Abiola promising to make him his running mate. Abiola was later pressured by SDP governors to select Kinigbe as his Vice-presidential running mate, in the June 12 presidential election.