N'Guessan joined the Secretariat-General of the FPI in 1990, and in 1994 he became Deputy Secretary-General. In January 2000, after a military coup in December 1999, he became Minister of Industry and Tourism under military leader Robert Gueï, serving in that position until October 2000. N'Guessan was the campaign director for FPI candidate Laurent Gbagbo in the October 2000 presidential election, and after Gbagbo's victory he was appointed Prime Minister.