Allied Bakeries announced a consultation into plans to close its Chester Road site in Saltney as part of an efficiency review in July.
The firm has now said it will shut the depot on 19 November.
The company said "every effort" would be made to help those people affected to secure alternative employment.
Allied Bakeries said in a statement: "We understand that this will be a difficult and unsettling time for our employees and their families and are doing everything we can to offer them support during this period."
The firm said affected staff could secure alternative roles in other parts of its business, including at its bakery in Stockport and a new local distribution operation.
Allied said the decision to close the depot "in no way reflects the commitment and efforts of those affected".
Alyn and Deeside MP Mark Tami said that, while Allied had discussed the possibility of redeploying staff in other parts of the business, this would probably not be ideal for "the bulk" of the workforce.
"We really have to concentrate on trying to ensure people get an opportunity to find alternative employment in the area," he added.
"We are fortunate that we do have a lot of quality employers in the area."
The bread firm behind brands Kingsmill, Allinson, and Burgen has announced it will shut a distribution depot in Flintshire, with up to 53 jobs at risk.