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.

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.

Motagua faced Atlanta United FC in the Round of 16 at the 2020 CONCACAF Champions League, where they couldn't advance after falling 1–4 on aggregated score.

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.