The Russian consumer protection agency said it is taking the company to court for selling foods that contain more fats and carbohydrates than are allowed by national regulations.
McDonald's did not immediately reply to a request for comment.
The move comes amid especially high tensions between Moscow and Washington over the Ukraine crisis.
The US has slapped an array of sanctions on Russia over its annexation of Crimea from Ukraine for allegedly supporting separatist rebels who are fighting in eastern Ukraine.
There is no demonstrable connection between the McDonald's lawsuit and the tensions, but the consumer protection agency, Rospotrebnadzor, has a history of actions that appear to dovetail with Russia's political agenda.
As tensions between Russia and Georgia escalated before their 2008 war, Russia banned the import of Georgian wine and mineral water - two of its major export products - for failing to meet sanitary regulations.
Last year, as tensions heated up over Ukraine's desire to sign a trade pact with the EU, Russia banned imports of chocolates made by the company of Petro Poroshenko, a tycoon who supported the EU deal and is now Ukraine's president.
Rospotrebnadzor said on its website that it brought the case after inspections of two of the company's restaurants in Novgorod.
According to the statement, some food was found with microbial contamination and several items had caloric values two to three times higher than allowed by national regulations.
Products that were mentioned for incorrect nutritional information were cheeseburgers, Royal Cheeseburgers - the local equivalent of the Quarter Pounder - fish sandwiches and several milkshake varieties.
The lawsuit asks that sale of McDonald's products that do not meet the regulations be declared illegal, but it was not clear what penalty the company could face. The two restaurants in Novgorod were to be fined 70,000 roubles (£1,237).
McDonald's prompted the anger of Russian nationalists earlier this year after it closed its outlets in Crimea.
The animosity is a far cry from the fascination that Muscovites had for McDonald's when it opened its first outlet in the Soviet Union in 1990.
Customers waited in hours-long lines to experience the efficient service and reliable availability of items - rare novelties in the Soviet era.
After the collapse of the USSR in 1991, other American and European chains staked out their own territory.
Russian malls now have food courts virtually identical to America's, except that Cinnabon, Sbarro and other familiar names are written in Cyrillic.