Martin tore his ACL in July, and his hopes of a return next year were dashed a couple of weeks ago following a training injury.
Recent scans confirmed Martin had suffered further damage to his reconstructed right knee, with the 24-year-old undergoing surgery on Thursday.
The injury will rule Martin out for all of next season, robbing Essendon of one of their best players.Â
"It's obviously a setback, but I have complete confidence in our medical and high-performance team and our long-term plan for me," Martin said.
"I'm feeling good post-surgery and I'm ready to take the time to build my knee back up and I know I'm in the best hands possible, and I'll attack this rehab with everything I've got to come back stronger."
In another blow, injury-plagued defender Jordan Ridley reportedly strained his hamstring on Friday in a bad sign to his build for 2026.
Ridley has been beset by soft tissue injuries over the past two years, with the club desperate to get to the bottom of the repeated setbacks.
The injuries to Martin and Ridley cap a busy week for Essendon after Zach Merrett, who wanted to be traded to Hawthorn during the off-season, stepped down as captain.