[5] In January 2018, Bonner was named as first team coach, working under manager Shaun Derry and assistant Joe Dunne, taking over the role from Mick Halsall.
In March 2020, Bonner was named permanent head coach of Cambridge United on a two-year contract until the end of the 2021–22 season.
[11] Due to the curtailing of the 2019–20 season caused by the COVID-19 pandemic, Bonner's first match as permanent head coach did not come for six months until Cambridge United knocked Championship side Birmingham City out of the first round of the 2020–21 EFL Cup.
Bonner's first full season as a manager was hugely successful for Cambridge United, both in team and personal honours.
[15] Bonner led Cambridge to a 1–0 away win to Premier League Newcastle United in the FA Cup third round in January 2022.