The Spoon Cafe on Nicolson Street made the announcement on social media that the new restrictions made it impossible to carry on.
The cafe, previously named Nicolsons, was revealed by Rowling in a BBC documentary as the place “where I wrote huge parts of the book” .
Since 2009, the premises have been called Spoon. A small plaque outside mentions the Rowling link, below the window where she once sat.
Spoon said on social media: “As with most businesses this year has been utterly crap for us.
“Spoon has existed as an independent cafe trading for over ten years in the heart of the city.”
It continued: "We have tried as hard as we can to keep going. We have persevered against a significant loss of business as well as having received no furlough of rent reductions.
"With the new restrictions announced we have been put in a helpless position. It breaks our hearts to say goodbye.
"Friday the 9th will be our last day. Pop by for one last coffee or just a chat.
"Thanks to all of you that have supported us through the years. We will miss you all.”
Customers flocked to the cafe’s Facebook page to pay tribute after the “heartbreaking” news.
Among them was Megan Duff, who said: “This is heartbreaking. Such fond memories of Spoon over the 7 years I lived in Edinburgh. Had always thought I'd be able to go back. So sorry to hear this news.”