Russia's food safety agency announced inspections at McDonald's fast-food chains in Sverdlovsk region, after closing down four branches in the capital Moscow.
The watchdog said the decision to temporarily close the Moscow outlets was related to sanitary violations but the measures come as political relations between Russia and the West have soured to their worst level since the end of the Cold War.
Among the closures in Moscow was the country's first McDonald's which opened on Pushkin Square as the Soviet Union collapsed in 1990. The fast-food giant has said the branch is its most popular in the world.
The agency, known as Rospotrebnadzor, said inspectors had discovered a number of sanitary violations at the Moscow branches and that it was reacting to customer complaints in Sverdlovsk.
"Checks were started due to complaints," said Natalya Lukyantseva, an agency official in the region, as quoted by Reuters news agency.
The moves come amid heightened tensions between Washington and Moscow over the crisis in Ukraine.
The United States and the European Union passed their toughest economic sanctions yet against entire sectors of the Russian economy in early August.
The allies have accused Moscow of backing the separatist rebellion in eastern Ukraine, providing weapons and manpower to rebel militias.
The US and EU measures targeted the country's defence, finance and energy sectors.
Moscow reacted to the sanctions by implementing a year-long import ban on a range of foods from the US, EU, Canada, Norway and Australia.
In addition to the food import sanctions, Russia's food agency has also threatened to ban a number of McDonald's products, including the Filet-o-Fish and Cheeseburger range.
It remains unclear how many restaurants in the region were being targeted for inspection.