The Bundesliga club have reached full agreement with Marseille over a transfer worth an initial €23m plus a further €2m in performance-related bonuses, according to Foot Mercato journalist Santi Aouna.
Medina, 27, is set to sign a five-year contract running until the summer of 2031 once the paperwork between the two clubs is finalised, with personal terms already understood to be in place. Leverkusen had seen an opening offer knocked back by Marseille before returning with the improved proposal that has now been accepted, having tracked the defender for some time, including during his previous spell at Lens.
The centre-back, who can also play at left-back, joined Marseille from Lens for around €20m last summer and made 26 appearances in all competitions for the Ligue 1 club last season, providing one assist.
His departure comes despite having a contract at the Vélodrome running until 2030, but Marseille chose not to stand in the way of a move Medina had reportedly given his approval to from the outset. The sale will provide a financial boost for the French club as they continue reshaping their squad this summer, with Marseille also close to selling goalkeeper Gerónimo Rulli to Manchester City.
Medina was part of the Argentina squad that reached the final of the 2026 World Cup, where they finished as runners-up, and has made 14 appearances for the senior national team, contributing one assist.
At Leverkusen, he will link up with fellow Argentina international Exequiel Palacios and is expected to become a key addition to Carles Martínez Novell's rebuilding project at the BayArena, with the club looking to strengthen their defensive options after finishing sixth in the Bundesliga last season.
Medina is due to travel to Germany to complete the formalities and sign his contract once his holiday concludes.