In the 2019–20 season, Fernandes played in both legs of the UEFA Europa League play–off round against RC Strasbourg, as he helped Eintracht Frankfurt win 3–1 on aggregate to send them through to the Group Stage. However, he found his first team place limited following an increase in the midfield position and was placed on the substitute bench as a result. By mid–September, Fernandes received seven starts for the club by the end of the year despite facing sidelined with suspension and injury. In the second half of the season, he was plagued by injuries that saw sidelined for months. The five-months interruption because of the COVID-19 pandemic gave him time to recover, and returned to training. It was announced 14 May 2020 that Fernandes would retire at the end of the season, bringing an end to a 15-year career. It wasn't until on 23 May 2020 when he made his first appearances for the Eintracht Frankfurt since December, captaining the club, as they lost 5–2 against Bayern Munich. Fernandes previously captained Eintracht Frankfurt earlier in the 2019–20 season, coming against Vitória de Guimarães on 3 October 2019. However, he suffered a calf injury that saw him sidelined for the rest of the season. Following this, Fernandes went on to make twenty–two appearances in all competitions. Two months after his retirement, he had an interview with Berner Zeitung and spoke about his retirement.