Seoane was appointed manager of reigning
Swiss Super League champions
Young Boys on 2 June 2018. Seoane, aged 39, was considered a surprise pick to succeed
Adi Hütter as coach, despite guiding
FC Luzern to third place in the
Super League in his first full management job. In his second season, Seoane led the club to a domestic double, delivering their 14th league title (their third in a row) and seventh cup title and first in over 30 years. In May 2021, it was announced that Seoane would coach
Bundesliga club
Bayer Leverkusen. In the
2021–22 season, he led Bayer Leverkusen to finish third in the Bundesliga, to be their best finish in seven seasons. However, he was sacked on 5 October 2022, due to his Leverkusen's poorest season start since their promotion in 1979. Leverkusen had won only one game, drawn two, and lost five games, resulting in only five points in their first eight games. In June 2023, he was named the new head coach of
Borussia Mönchengladbach, starting from the 2023–24 season. He was sacked in September 2025. On 31 October 2025, he returned to
BSC Young Boys, signing a contract until summer 2028. ==Personal life==