The company could now face legal action.
General manager Daniel McArthur confirmed that he had received a letter from the Equality commission for Northern Ireland after refusing to make the cake.
In a statement on the company website, Mr McArthur explained his decision, and said: “The directors and myself looked at it and considered it, and thought that this order was at odds with our beliefs.”
Speaking to The Guardian about the repercussions of his actions, he said: “We thought that was the end of it, but approximately six weeks later we received a letter from the Equality commission.
“The commission’s letter said that we had discriminated against the customer on the grounds of his sexual orientation.”
Andrew Muir, who is Northern Ireland’s first openly-gay mayor, has supported action taken against the bakery.
“Businesses should not be able to pick and choose who they serve,” he said.
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