Up to 1,400 jobs have been saved after the company that owns Poundbakery and Sayers was rescued from administration.
A new company, Sayers and Poundbakery Ltd has been formed but 11 stores will close making 100 staff redundant.
A spokesman for the administrators Grant Thornton UK said: "We are doing everything we can to support these employees."
Prior to administration, the Bolton-based parent firm, Sayers The Bakers Ltd, had a turnover of £50m.
The new company will operate the main bakery and distribution centre in the town as well as the majority of its 167 Sayers, Poundbakery and Poundcafé stores across Northern England, North Wales, Yorkshire and the Midlands.
Sarah O'Toole, advisory partner at administrators Grant Thornton UK LLP said: "We are delighted to have concluded the sale which preserves a significant number of jobs at this long established business.
"Unfortunately, a number of redundancies have been made across 11 closed stores at a particularly difficult time of year and we are doing everything we can to support these employees."
The new firm will be run by the former management team led by Mark James and David Silvester.
In a statement, they said: "We'd like to wholeheartedly thank the loyal staff, suppliers and customers for their continued support as we enter into the next stage of this historic brand's future."