The former Premier League winner won’t be at the helm for tonight’s re-arranged game with Barrow.
Moors have won just once in seven matches and have slipped out of the National League promotion positions.
Assistant manager Gary Whild and coach James Quinn will take charge of this evening’s match.
Chairman Darryl Eales said: “Tim has made an invaluable contribution to the development of Moors and his legacy will be enshrined in Moors history forever.
“He has been an absolute pleasure to work with and he has done a magnificent job for the club. Our progress under his stewardship has been fantastic and he leaves a great foundation for future success.
“On behalf of the Board, all staff and I am sure all fans, I’d like to thank Tim for everything. He leaves the club with our best wishes for the future and will always be sure of the warmest of welcome at Damson Parkway.”
Flowers told the club’s website: “It is with immense pride that I leave Solihull Moors Football Club. The journey that we’ve been on in the last two years or so has been quite remarkable.
“I would like to thank my staff - Gary Whild, James Quinn, Darren Acton, Craig Cope, Steve Hensel, Mick Kemp and Ian Hutton for their tireless effort, help and support throughout this journey.
“I’d like to thank Darryl who has been a great source of support and also a good friend. Also, the entire board of directors who have helped me over those two years.
“I wish the club all the very best in their quest for Football League status and I will remain an avid watcher and fan.
“Finally, to the ever-growing Solihull Moors fanbase for their support at home and away.
“Their backing has been a huge help in us picking up points, making our stadium an incredibly difficult place to come and the band that follow us away from home have been key in getting us over the line in a number a games.”