The fire which happened in August was followed by a 100m cordon closed 14 shops within its perimeter as a safety precaution and in response the amount of shoppers in the city has slumped.
The bakery on Royal Avenue which is 200ft from the clothing chain's flagship store was in headlines last week after being vindicated of discrimination on the grounds of sexual orientation for refusing to print a message on a cake endorsing same-sex marriage.
Christians across the world had been praying for a victory for the case despite two initial losses at the County Court and the Court of Appeal.
Speaking to the Belfast Telegraph on the decision not to renew the lease, general manager Daniel McArthur said: "It simply comes down to the figures
"Belfast city centre isn't busy enough - our other shops are much busier.
"I am pleased to say there will be no job losses."
Last year, the bakery reported that their profits had grown to £1.5million.
What should happen to the Primark store has divided opinion with businesses saying that in order to salvage the upcoming Christmas trade, the listed building should be pulled down.
Primark has donated £500,000 to Belfast City Council to help affected traders.
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