Bakker started her managerial career with Dutch side ASV Wartburgia [nl].
In 2017, she was appointed as an assistant manager of Dutch side Excelsior Rotterdam, before being appointed as manager of the reserve team of Dutch side AFC Ajax in 2022.
Two years later, she was promoted to manager of the club's first team, helping them win the league and 2023–24 KNVB Women's Cup.
[1] Despite this, she left them at the end of the 2023–24 season because of communication problems.
[2] Ahead of the 2024–25 season, she was appointed manager of Italian side AC Milan.