Flowers has been keeping himself busy with goalkeeper coaching and media work after his job at Queens Park Rangers ended.
The 43 year old will officially take charge of the Conference North Club on Sunday with Steve Wynn in charge of the team for Saturday's game at Nuneaton Town.
The job has come about following the dismissal of Chris Brindley who was in charge last season when the Marston Road side were knocked out of the FA Cup by Coventry Sphinx.