On 23 July 2010, Filipe Luís signed for five years with Atlético Madrid for an undisclosed fee, reported to have reached €12 or 13.5 million. His official debut came on 26 September at home against Real Zaragoza, where he set up compatriot Diego Costa for the game’s only goal, receiving Player of the match accolades. In his first season, Filipe Luís constantly fought for first-choice status with youth graduate Antonio López. On 10 April 2011, he scored his first goal for the team in a 3–0 home win over Real Sociedad. On 17 January 2013, he netted the second in a 2–0 defeat of Real Betis in the Copa del Rey, and also played the full 90 minutes in the final of the latter competition against Real Madrid, which ended with a 2–1 triumph at the Santiago Bernabéu Stadium. Filipe Luís made his first appearances in the UEFA Champions League in the 2013–14 edition, helping the Colchoneros secure first place in Group G by scoring once in a 4–0 home rout of FK Austria Wien. During the league campaign, he was part of a stellar backline that only conceded 26 goals in 38 games as Atlético won the league title for the first time in 18 years. Additionally, he took part in ten matches in the Champions League, including the 1–4 final loss to Real Madrid in Lisbon, being subsequently voted the best defender in the Spanish League alongside teammate Miranda and Real Madrid’s Sergio Ramos. On 28 July 2015, Filipe Luís re-joined Atlético Madrid on a four-year deal for an undisclosed fee. He made his return to the team on 22 August as they opened the season with a 1–0 home victory against newly promoted UD Las Palmas. In the 3–0 win in the reverse fixture the following 17 January, he scored his first goal since returning. On 30 January 2016, Filipe Luís was sent off in the first half of a 1–2 loss at FC Barcelona for a challenge on Lionel Messi, and teammate Diego Godín was later also dismissed. The duo escaped criticism by manager Diego Simeone, but Filipe Luís was subsequently handed a three-match ban. He continued being an undisputed starter during his spell at the Vicente Calderón Stadium. In March 2018, after a collision with FC Lokomotiv Moscow’s Eder in a Europa League tie, Filipe Luís broke the fibula in his left leg, initially being thought to miss the rest of the season and thus the 2018 FIFA World Cup but making a recovery in two months. He ended his second stint at Atlético upon the expiration of his contract, on 30 June 2019.