The American is still some way off a first-team comeback but will now pick up his own individual rehabilitation programme at Euxton after spending several months at a specialist centre in the United States.
Holden, who made just one appearance last season, has spent 18 months struggling to overcome a knee injury, and will not be rushed back into action.
But his re-appearance at the training ground should lift spirits after a difficult week in the aftermath of Owen Coyle's departure as manager.
The US international has featured just once - against Aston Villa in the Carling Cup - since being stretchered off at Old Trafford in March, 2011, following a heavy challenge by Manchester United defender Jonny Evans.
Screws inserted to stabilise that injury then caused damage to cartilage and a second breakdown last September.
Since that operation, Holden has largely been working with specialists in Delaware to get himself in shape for a comeback.
And speaking this weekend, his former manager Coyle admitted the midfielder's absence hastened the club's dramatic fall from grace over the last 12 months.
“Stuart was irreplaceable,” said the former Whites boss. “We had many gifted players at the club but he was the complete midfielder. Some can run, some can pass, some can tackle. He has the lot.”
Meanwhile, it looks increasingly likely that the caretaker management team of Jimmy Phillips, Sammy Lee and Julian Darby will lead the Whites into battle against Bristol City on Saturday.
The club are in no rush to appoint a replacement for Coyle and have assembled the experienced trio to take care of matters until the right man can be found.
It is understood a shortlist of names has been drawn up by chairman Phil Gartside and that informal conversations have been conducted with some of the candidates.
But with number one choice Ole Gunnar Solskjaer stating that he wants to remain at Molde at least until the end of the Norwegian league season on November 18, it now comes down to whether Wanderers want to bide their time for another month.