Babangida's fortunes started to change towards the end of 1998. Having missed the start of the season with malaria, Babangida gradually lost his starting line-up position as Morten Olsen was looking to improve on the team's inconsistent performances both in the domestic league and in Europe. Babangida started two of his team's opening Champions League games. The European season, however, ended in disappointment as Ajax finished bottom of their group behind Olympiacos, Dinamo Zagreb and Porto. Overall, Babangida appeared in 18 league games for Ajax that season, starting only seven. He didn't feature in the Dutch Cup final where Ajax managed to retain the trophy after beating Fortuna Sittard in the final.