In the opening game of the 2018–19 season against SC Freiburg, Fernandes was given the captaincy for the time in his Eintracht Frankfurt's career in absent of David Abraham, as the club drew 1–1. It wasn't until on 23 September 2018 when he scored his first goal for the club, in a 1–1 draw against RB Leipzig. Fernandes was involved in the first team for the first two months to the season until he suffered a knock that saw him missed one match. Following his return from injury, he continued to remain in the first team regular, playing in the midfield position. As a result, Fernandes signed a one–year contract extension with Eintracht Frankfurt, keeping him until 2020. In continuous absent of Abraham due to injury, Fernandes resumed as the captain of Eintracht Frankfurt between December and April.However, he later missed five matches in the second half of the season, including a second bookable offence, in a 3–1 loss against FC Augsburg on 14 April 2019. At the end of the 2018–19 season, Fernandes went on to make thirty–seven appearances and scoring once in all competitions.