After finishing in third place last season, the club were looking for their 8th and 9th league title.

After manager Ramón Maradiaga took charge of the Honduras national football team, the club hired Mexican coach José Treviño with whom they were able to win the Apertura tournament.

[1] With the win, Treviño returned to Mexico and assistant coach and former striker Luis Reyes managed to repeat and won the Clausura tournament.

Internationally, Motagua faced Comunicaciones F.C., Juventus FC, C.D.

Luis Ángel Firpo and Deportivo Saprissa in the 1999 UNCAF Interclub Cup, but were unable to proceed from the first round.