Courts ordered three McDonald's restaurants in Moscow to be closed for the maximum term of 90 days on Wednesday on health grounds in a case widely seen as retaliation against Western sanctions.
The three Moscow restaurants include one located in the shadow of the Kremlin and the first McDonald's restaurant to open its doors in the final years of Communism, becoming a symbol of Russia's gradual acceptance of the West.
But the decision is set against retribution by Russia for sanctions by the West over Russia's support for separatists fighting in eastern Ukraine.
Last week the consumer safety agency Rospotrebnadzor ordered the Moscow restaurants closed. And reports circulated that the government had ordered inspections of all of the US burger chain's more than 430 locations across the country.
"We disagree with the court ruling and will appeal," McDonald's said in a statement.
"The rulings were unfounded, the court imposed the maximum penalty... but there was no justification for this," McDonald's lawyer Maxim Titarenko was quoted as saying by Russian news agencies.
"The violations which Rospotrebnadzor cited have either already been eliminated or are in the process of being eliminated," he added.
A court also ordered closed a restaurant in Yekaterinburg for 85 days, Interfax news agency reported on Wednesday.
McDonald's said Wednesday another one of its Moscow sites has been ordered closed following "mass inspections" of its restaurants.
A restaurant has also been closed in the southern city of Stavropol.
Officials have denied the company is being specifically targeted.
"These inspections are not political in any way," Rospotrebnadzor chief Anna Popova said this week. "Russian consumers have the right to be served safe and quality food at all public establishments."
While ostensibly for health reasons, the move against McDonald's came close on the heels of the West ratcheting up sanctions on Moscow for its role in the Ukraine crisis -- and Russia banning most US and EU food imports in retaliation.
Russia has a long history of using sudden food safety concerns as a political weapon against unfriendly states.
McDonald's did not win any friends in the Kremlin by closing its restaurants in Crimea after Russia seized the Black Sea peninsula from Ukraine earlier this year.
While McDonald's is a symbol of American culture, the company has made huge efforts to build up its local supply chain and says it buys 85 percent of the food it serves in Russia inside the country.