Fears have been raised the woman, who worked for the company for 21 years, may have fallen victim to Covid-19.
Another employee at the factory, which produces 500million Yorkshire puddings a year, was left seriously ill in hospital after contracting the virus.
The employee who died worked at the firm’s factory in Hull where the previous cases were discovered earlier this month, HullLive reports.
Her cause of death is yet to be confirmed, although it is believed the virus was responsible, according to reports.
Bosses described her as "an important member" of staff at the workplace, which is believed to employ around 400 people.
They said they have "followed and gone beyond the guidance" set out by public health bodies when confirming the earlier cases.
A spokesman for Aunt Bessie's said: "We are all saddened about the death of our colleague, and our thoughts and condolences are with her family and friends at this time.
"She was an important member of our team for 21 years and we will do everything we can to support her family.
"As a mark of respect, today we won’t be running the shift our colleague worked on, so that friends and colleagues have time to mourn and remember her."
After the outbreak earlier this month, the factory was left running at reduced capacity after the company deep cleaned it.
In a statement at the time, Aunt Bessie's said: "Currently, our Aunt Bessie's factory has a small number of coronavirus cases, but PHE has repeatedly complimented us on our social distancing measures and our proactive approach to ensuring that our colleagues are safe and well.
"The health and welfare of our employees is our number one priority.
"We acted early and decisively in March to implement new procedures and have strict protocols at all of our sites, including our Hull Aunt Bessie's factory, to reduce the risk of coronavirus spreading amongst our employees."
A Greggs depot near Leeds was last month forced to shutdown after around 20 staff members were infected.
Meanwhile, in Norfolk hundreds of workers were forced to self-isolate after the disease was detected at a Banham Poultry factory.