On 24 May 2018, Rodri returned to Atlético after the club reached an agreement with Villarreal for his transfer. He signed a five-year contract with the Madrid side, for a fee in the region of €20 million plus 5 million in variables. He made his debut on 15 August in the 2018 UEFA Super Cup in Tallinn, playing the first 71 minutes of a 4–2 extra-time win over city rivals Real Madrid.