As coach Diego Vásquez renewed his contract, he led the team for his 14th consecutive tournament. After two straight defeats against C.D. Olimpia and Nicaraguan side Real Estelí FC at the 2020 CONCACAF League, F.C. Motagua was unable to qualify to their second straight CONCACAF Champions League.[2] Only one month later, the team was eliminated from domestic contention (Apertura) against Olimpia in the so called "Final de Liguilla" (Playoffs finals).[3] In May 2021, Motagua was unable to reach another final as they lost to Olimpia in the Clausura Playoff final series in penalty shoot-outs.[4]
Kits
The 2020–21 home and away kits were published on 25 September, one day before their debut in the Apertura tournament. Unlike previous seasons, no third kit was released.
This is a list of players that were playing for Motagua during the 2020–21 season and were called to represent Honduras at different international competitions.
Note: For the first time, F.C. Motagua was allowed to use the temporary five substitutions rule proposed by FIFA in order to lessen the impact of fixture congestion caused by the COVID-19 pandemic. A late goal from Gonzalo Klusener in injury time, gave Motagua the first win of the season.
Note: Referee Jefferson Escobar officiated a F.C. Motagua's game for his first time. Midfielder Omar Elvir was honored by the club for reaching 300 games with the institution.
Note: This became the second ever F.C. Motagua's victory at this venue and the largest away win since October 1999 (2–7 v C.D. Federal). Youngster Arnold Álvarez made his debut wearing the jersey number 42.
Note: Due to the passing of Hurricane Eta, weeks 11 and 12 were postponed. F.C. Motagua obtained their largest ever victory at this venue. Forward Rubilio Castillo reached 101 goals for the club in all official competitions.
Note: Youngsters Danilo Palacios and Andy Hernández made their professional debuts wearing jerseys #44 and #54 respectively. With 39 league goals, Paraguayan Roberto Moreira became the foreign player with most goals for Motagua, surpasing Chilean Mario Yubini (38).
Note: Defender Cristopher Meléndez scored his first official goal for the club. F.C. Motagua finished the regular season in 2nd place in their group and qualified to the play-off stage.
Note: Midfielder Jesse Moncada made his official debut with the club. For the first time in league's history, F.C. Motagua defeated C.D. Marathón in four consecutive away games.
Note: Due to 10 players from C.D. Real Sociedad resulting COVID-19 positive, this match was postponed from the original kick off day. Midfielder Iván López scored his first official goal for F.C. Motagua. Forward Roberto Moreira reached 100 league appearances with the club.
Note: Striker Gonzalo Klusener scored his first hat-trick for the club. Goalkeeper Hugo Caballero made his official debut as entering the field as substitute in the second half. With the win, F.C. Motagua increased their record to four consecutive away victories against Platense F.C.
Note: This became the second time in history that F.C. Motagua lost a championship in penalty shoot-outs, and the first one against C.D. Olimpia. Midfielder Raúl Santos reached 100 league appearances with the club.
Note: F.C. Motagua and C.D. Olimpia faced in international contention for third time in history, the first two being played back in 1979. With the loss, Motagua failed to qualify to their third straight CONCACAF League semifinals.