The Kenilworth born keeper had been assistant manager at Loftus Road under first former City boss Iain Dowie and then caretaker Gareth Ainsworth.
However, new R's boss Paulo Sousa has appointed Bruno Oliveira as his assistant coach and Flowers left the club today.
A statement on the QPR official website said: "We would like to place on record our thanks to Tim and wish him all the success in the future.
There has been no news as to whether former CCFC performance director John Harbin still has a job or not.
Iain Dowie has been linked with the vacant manager's job at Swndon Town. The BBC have said that the former City boss is in the frame with Aidy Boothroyd, John Ward and Ian Holloway.