Genius Foods, which makes gluten-free bread products, said "recent changes in its European business" resulted in a decision to shut its Main Street plant by late September.
In April the company announced it was to shed about 115 posts across its entire business, with 70 axed in Hull.
Last year, the Edinburgh-based bakery was ranked among the most valuable Scottish brands.
Genius Foods said several of its European customers had decided to offer unbranded bread and had switched to another supplier.
The Hull factory focuses on production for the international market and, as a result of the move, "the production volumes in Hull will be sufficiently reduced to make continuing operations at the site unviable", Genius said.
Chief executive Jeremy Bradley said: "We fully understand the shock and disappointment of this announcement for all of our employees.
"It has been necessary to respond to the change in activity at Hull, and the priority of the entire Genius team is to do everything possible in the coming weeks and months to support the hard working and dedicated employees at the site.
"We have put in place a comprehensive package of practical support and advice to help secure alternative employment opportunities as quickly as possible."
Genius said its Scunthorpe factory was unaffected by the change and that it would be creating 27 roles at its production site in Bathgate, West Lothian, where it was moving its export side of the business.
A bakery firm is to close its factory in Hull with the loss of 68 jobs.