Willie Earl Banks has managed the city for the past six years.
His resignation comes amid recent moves by city commissioners to vote him out.
Leon County Finance Director Bill Bogan has been asked by Quincy city officials to help out in a temporary manner until the vacancy is filled.
"I am a loyal employee. I was a loyal employee of 22 years and I worked hard with the city. I know that many on the board felt as if being under my watch and having had a cash flow problem, that it was my fault for that," says Banks.
"I'm looking forward to working with the people of the city of Quincy and seeing what I can do to assist and help out and make that government what it aught to be," adds Bogan.
Banks, a Quincy resident, says he wants to fill another city manager position, even if it means relocating to another city.