The 37-year-old broke his leg whilst on the slopes and spent nine-months sidelines.
But the club have now confirmed he has returned to training alongside goalkeepers Tom Ritzy Hulsmann and new signing Daniel Perertz.
A statement on Bayern's website, read: "Good news from Sabener Straße: Manuel Neuer is back with the FC Bayern goalkeeper team on the pitch.
"In Monday morning's training session for the players who didn't start against FC Augsburg on Sunday, the 37-year-old captain completed a session with his goalkeeping colleagues for the first time since breaking his lower right leg.
"Neuer has been sidelined since sustaining the injury in December 2022 but has now taken the next step on the comeback trail."
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Israeli-born Perertz recently joined Bayern Munich from Maccabi Tel Aviv, and will compete with Neuer for a place in the starting XI.
Hulsmann, at just 19, is another who will train with the first-team after signing his first professional contract with the Bavarian giants.
Last December in a post on Instagram, Neuer announced his injury with a picture of himself a hospital bed with his leg in a cast, and his left hand also bandaged up.
"Hey guys, what can I say, the end of the year could have definitely gone better..." said the 36-year-old.
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"While I was trying to get my head clear while ski touring, I suffered a lower leg fracture. Yesterday's surgery went well. Many thanks to the doctors!
"However, it hurts to know that the current season is over for me. Take care! Your Manuel."
Neuer featured for Germany at the World Cup in Qatar, only for the four-time winners to suffer an embarrassing group stage exit prior to his accident.
Neuer's future at Bayern Munich has been the subject of speculation since his injury, with the experienced Sven Ulreich taking his place alongside with Yann Sommer.
Sommer, though, has since been sold to Inter Milan, while Ulreich remains in the squad.
Another goalkeeper in the ranks meanwhile, Alexander Nubel, is spending the current campaign on-loan at Stuttgart.