Coach Diego Vásquez renewed his contract, he will be leading the team for his 12th consecutive tournament. Vásquez reached 240+ consecutive games as Motagua's manager, a club's and league record. In August 2019, the club announced the re-signing of defender Emilio Izaguirre, who returned to Motagua almost a decade later after his successful venture at Celtic F.C.. On 25 September 2019, the club officially qualified to the 2020 CONCACAF Champions League through their participation at the 2019 CONCACAF League.[2] On 31 October, Motagua qualified to their 2nd straight CONCACAF League final after defeating Alianza F.C. with a 4–1 aggregated score. However, in the final series, they weren't able to conquer the tournament as they lost to Deportivo Saprissa with a 0–1 aggregate score.[3] In the Apertura tournament, Motagua was able to qualify to the Final 5 Stage (Pentagonal), however felt short against C.D. Olimpia and failed to qualify to their seventh straight final series.[4]
The 2019–20 home, away and third kits were published on 27 June. On 1 October, the club released an all-pink jersey to support breast cancer awareness.
This is a list of players that were playing for Motagua during the 2019–20 season and were called to represent Honduras at different international competitions.
Note: Midfielder Óscar Salas made his official debut with the club. Defender Félix Crisanto reached 100 appearances with F.C. Motagua in his loan return from Lobos BUAP. Meanwhile, his cousin Wilmer Crisanto reached 200 appearances with the club.
Note: Defender Emilio Izaguirre returned to F.C. Motagua after almost a ten-year career in Europe. Meanwhile, youngster made his official debut for the club.
Note: This game was scheduled to be played on 17 August, but due to the riots caused by the fans inside and outside the stadium, the game was played on November 3rd. C.D. Olimpia as home club, opted to move the game to San Pedro Sula. It was the first derby at this city since 17 December 2006.
Note: F.C. Motagua obtained their first away victory of the season. Defender Marcelo Pereira reached his 100th appearance for the club. Youngster Jack Baptiste reappeared since February 2019 after his loan return from Loudoun United FC.
Note: Forward scored his first goal of the season in a game which was played under an electrical storm most of the second half. With the win, F.C. Motagua reached the top of the standings.
Note: As suggested by the National Security Department, this so considered high risk derby had to be taken outside Tegucigalpa. F.C. Motagua responded to the advise by taking the match to Comayagua. With the loss, Motagua dropped to third position.
Note: This game was pushed one week later to allow time to previous postponed games. It was the first F.C. Motagua's visit to Tocoa since March 2018. Defender Henry Ayala made his official debut for the club.
Note: This game was pushed one day further; however F.C. Motagua only had 48 hours of rest from their previous match. Winger Wilmer Crisanto scored one goal and made three assistances. Motagua reverted a 0–2 disadvantage in the 23rd minute.
Note: F.C. Motagua was forced to move this match outside Tegucigalpa. Despite the victory, they were 3 goal difference short against C.D. Olimpia in the Pentagonal stage, thus missing their chances to qualify to their seventh straight final series.
Note: For the third time in history, F.C. Motagua starts a tournament with an away victory at Estadio Excélsior, the first two happening in 2007 and 2016. During the second half, midfielder Wilmer Crisanto suffered racial chants from the local crowd.
Note: Due to repairs at Estadio Tiburcio Carías Andino, this game was moved to Danlí. It was the fourth time F.C. Motagua faced C.D. Marathón at this venue, with a previous record of 1–2–0 (6:4) to Motagua. Forward Gonzalo Klusener made his official debut with the club, scoring the only goal for Motagua.
Note: Coach Diego Vásquez sent an alternative lineup due to their upcoming match at Atlanta United FC. It was the first scoreless tie of the tournament. Midfielder Walter Martínez reached 100 appearances with the club.
Note: Due to a musical concert, the match was played at an unusual time. Defender Reinieri Mayorquín reached 200 league appearances with the club. F.C. Motagua swept Real C.D. España in the regular season for the first time since 2009.
Note: Due to the coronavirus pandemic, this game was played behind closed doors. Also, this became the fifth straight Honduran Superclásico played outside Tegucigalpa. With a 4–1 victory, this became the fifth time in history that F.C. Motagua defeated C.D. Olimpia by a margin of 3+ goals and the first time in Liga Nacional.
Note: F.C. Motagua advanced to the quarterfinals thanks to a 3–2 aggregated score. Due to a ban to Estadio Tiburcio Carías Andino, CONCACAF decided to relocate the game to San Pedro Sula behind closed doors.
Note: This was the first ever encounter between these two clubs, and the first F.C. Motagua's visit to this venue since August 2018. With the win, Motagua obtained the sufficient points to qualify to the 2020 CONCACAF Champions League.
Note: With a 2–0 score on aggregate, F.C. Motagua qualified to the semifinals. Defender Raúl Santos returned from his long-lasting injury and played again since 13 March 2019.
Note: With a 4–1 score on aggregate, F.C. Motagua qualified to their second straight CONCACAF League final. Marco Vega and scored their first ever international goal with the club.
Note: This was a rematch between these two clubs since the 2007 UNCAF Interclub Cup finals. F.C. Motagua lost at international level again after seven games, their second longest streak.
Note: It was the first ever F.C. Motagua's visit to Fifth Third Bank Stadium. With a 1–4 aggregate, the club was unable to advance to the quarterfinals.
By round[]
Round
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
Ground
H
A
H
A
A
H
H
A
A
H
H
A
H
A
A
H
A
H
A
H
H
A
A
H
A
H
A
H
H
A
H
A
A
H
A
H
Result
W
L
W
D
L
W
W
W
W
W
W
L
L
W
L
D
D
D
W
W
D
L
W
W
W
W
D
L
D
W
W
Position
3
4
3
4
3
3
3
3
2
1
1
2
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
3
Source:[citation needed] A = Away; H = Home; W = Win; D = Draw; L = Loss; P = Postponed
Óscar Salas
Loudoun United
BUAP
Celtic
Gonzalo Klusener
Tondela
Roberto Moreira
66
San Carlos 
73
60
Municipal Limeño 
