Margetson injured his knee in training on September 16th and has since had surgery on the knee and his back to remove two discs.
"A lot of my problem is down to the knee," Margetson told the Echo.
"That injury altered my gait slightly and that didn't help my back. That became the main problem and I had two discs taken out.
"I've had my two operations and I'm going through rehabilitation. I'm hoping to be back fit by the start of January and then I'll be having a word with the manager about my future."
Neil Alexander has been No.2 to Tony Warner while Margetson has been out.
City's other long term injury is Gary Croft. The full back is recovering from cruciate ligament damage and at best hopes to be able to play in April.