Nick's Pizza Bar, which opened in December 2016, has now been placed into voluntary liquidation.
The announcement comes after the celebrity chef closed his Cook School in the city at the end of June, again as a result of the downturn in the north east economy.
The closure of the pizza bar means Nairn - who found fame on the popular BBC programme Ready Steady Cook - no longer has a presence in Aberdeen.
When Nairn shut that business a month ago, he had hoped to expand the pizza bar as both enterprises were based in the same city centre building at Back Wynd, formerly St Nicholas Kirk's old church hall.
However he said despite recent investment in marketing the pizza restaurant, and extending its opening hours, it was not viable as a stand-alone business.
Five full time members of staff were affected - with Nairn breaking the news in person to them on Monday morning.
Nairn, who became Scotland's youngest chef to win a Michelin star in 1991, said he had taken the decision to close the restaurant "with regret".
He stated: "I had always wanted to expand into Aberdeen and the business had years of success with a loyal customer base. However, the downturn in the oil and gas industry hit the economy in the north east leaving people with less money to spend on eating out.
"It's with regret that I've had to make the decision to close my business in Aberdeen where I have enjoyed having a presence.
"I'd like to thank everyone who has worked with us in Aberdeen, and all our customers and suppliers with whom we have had an excellent relationship."
The closure of the cook school and pizza bar come after the chef was assaulted outside the premises in December 2017.