[3] Manning later returned to Woodbridge, followed by spells with Wroxham, Melton St Audrey and Ipswich Wanderers, before retiring from football to concentrate on coaching.
[5][6] Staying within City Football Group, in July 2020 Manning was named head coach of Belgian First Division B club Lommel SK, where he led the previously bottom of the table side to a third-placed finish at the end of the 2020–21 season.
[10] Following a poor start to the season that found his side in the relegation zone, Manning was dismissed on 11 December 2022,[11] having accumulated just fifteen points from twenty matches.
[14] On 7 November 2023, Manning, together with his assistant Chris Hogg, departed Oxford United and joined EFL Championship club Bristol City as the head coach, signing a contract until June 2027.
[17][18] He has a reputation for developing young players, having spent much of his early coaching career working with the academy sides of West Ham United, Ipswich Town and New York City FC.