At the beginning of the 2016–17 season, new manager Peter Bosz included Van de Beek in the Ajax squad for the UEFA Champions League qualification match against Greek club PAOK for a couple of reasons: Bosz was impressed by Van de Beek's performance during pre-season friendlies in Austria, Riechedly Bazoer was injured and Nemanja Gudelj was suspended. On 26 July, he made his Champions League debut against PAOK, starting in the 1–1 draw. While playing for the reserves during the season he and Abdelhak Nouri were the only players who were given more than a seven rating on average by "Voetbal International". In November, he was included in the Europa League Team of the Week for his performance against Panathinaikos. He was a part of a midfield trio with Nouri and Lasse Schöne. Van de Beek replaced Schöne in the 70th minute of the Europa League final against Manchester United, with Ajax losing the match 2–0.