Holden returned to action earlier this month, but after a routine followup surgery, it was determined the American midfielder would miss another six months.
On Tuesday, it was announced that Holden will be out for six months following a routine followup operation on his injured knee. It was initially thought he would only be sidelined for only six weeks.
"It is a big, big blow for Stuart because he has worked so hard after he sustained the injury, but obviously the most important aspect is to ensure Stuart's well being and that's what we are focused on," Bolton manager Owen Coyle told the team's website.
The 26-year-old Holden suffered an anterior cruciate ligament injury on his right knee in March following a tackle by Manchester United defender Jonny Evans.
The former Houston Dynamo midfielder made his comeback from injury against Aston Villa earlier in September, but he will now have to wait until next spring to play again."Floored, devastated, gutted, just a few words I can think of. I will continue to fight and I'm ready for another tough journey," Holden wrote on his Twitter account.
Coyle revealed the followup operation could have been delayed until next summer but the decision was made to do it right away. "After followup consultations with the specialists we have brought the date forward," the coach said.