On 20 June 2019, it was confirmed that Neestrup had been appointed as the manager of
Viborg FF for the upcoming season. In his first season at the club he guided the team to a third place in the
2019-20 Danish 1st Division. On 22 December 2020, it was announced that Neestrup would leave Viborg at the end of the year and return to
F.C. Copenhagen as assistant manager of
Jess Thorup. He left Viborg in 1st place in the
2020–21 Danish 1st Division. He was replaced by
Lars Friis, who would go on to win the Danish 1st Division and secure promotion to the
Danish Superliga. On 20 September 2022, Neestrup was announced as new manager of F.C. Copenhagen following the sacking of
Jess Thorup. Despite being placed 9th out of 12 and being 10 points off 1st place when he took over, Neestrup still eventually guided the club to win the
Danish Superliga and the
Danish Cup. On 12 December 2023, he guided them to the
knockout stages of the Champions League, being placed second in a group with
Bayern Munich,
Galatasaray and
Manchester United. In the
2024–25 season, Neestrup and Copenhagen won double again, beating
FC Midtjylland by just a single point in the league and beating
Silkeborg IF in the cup final. In the
2025–26 season, Copenhagen missed the championship group for the first time in the modern Superliga format. After losing the two opening matches in the relegation group to
Odense Boldklub and
FC Fredericia, Neestrup was fired and replaced by
Bo Svensson. At the time Copenhagen were without a win in 8 matches, which was the most of any team in Superliga. In the
Champions League Copenhagen reached the league phase, where they would go out in 31st. They got two wins against
Kairat Almaty and
Villarreal CF. ==Managerial statistics==