The Apertura started on 7 August, but due to its participation in the 2011–12 CONCACAF Champions League, their first official game was played on 28 July 2011.

Three days later, on 19 September, Mexican coach José Treviño arrived as new manager for the rest of the season;[10] while Colombian striker John Palacios left the team just one month after his signing arguing differences with teammates.

[11] On 22 September, the club released a pink jersey to be worn on all the games from October, in a way to support the fight against breast cancer.

[12] On 3 October, striker Jerry Bengtson appeared 50th on The World's Top Goal Scorer 2011 list published by the IFFHS.

Marathón in a neutral venue due to the incidents occurred on 9 October at the Estadio Tiburcio Carías Andino in the Honduran Superclásico against C.D.

España 2–0 at Tegucigalpa, breaking their own 1974 record for the longest unbeaten start in a season,[20] streak that lasted until 5 May totaling 19 games undefeated.

[22] As second placed at the end of the regular season, Motagua obtained an automatic ticket to the semifinals; the opponent was decided from the previous round, where Marathón beat Vida.

Once in the semifinals, Motagua were unable to surpass Marathón and lost 0–2 on aggregate score,[23] this being the second consecutive time that they were prematurely eliminated.

[39] Once in the Group phase, things went upside down for Motagua and on 22 September, they were mathematically eliminated from quarterfinal contention after losing 0–2 against Monarcas Morelia at Estadio Tiburcio Carías Andino.

[40] At the end of the group phase, Motagua not only were eliminated, but finished last with zero points with a sixth straight loss.