Trade relations between Turkey and Russia have traditionally been strong but these could be one of the first areas to be damaged from a Russian retaliation.
On Thursday, Russia's Agriculture Minister Alexander Tkachev tasked the country's food agency with "reinforcing control over supplies of agricultural produce and food from Turkey," AFP reported, saying that Russia had found multiple cases of Turkish produce not meeting Russian standards.
He noted that Turkish vegetables account for some 20 percent of vegetable imports to Russia and the country could opt to buy produce elsewhere. It also said it could re-direct wheat exports from Russia to Turkey (one the largest buyers of Russian wheat) to elsewhere in the Middle East.
In 2014, according to Turkish foreign trade statistics, exports to Russia were worth $5.9 billion while imports from Russia were worth $25.2 billion.
Erdogan said only in September during a cordial meeting with Putin that Turkey's goal was to raise that bilateral trade volume to $100 billion by 2023. At that meeting, Putin said Russia was "very satisfied with the development of bilateral relations. Our trade and economic relations continue to diversify, investment on both sides also increases," according to news network Russia Today.
The Kremlin said Thursday that it had no plans to place an embargo on food imports from Turkey, according to Reuters, and said it was not considering sanctions.
Although trade relations are now on shaky ground, analysts were sanguine about the long-term relationship. Tina Fordham, chief political analyst at Citi, said that "trade and commercial ties between the two countries are significant," given Russia's energy provision for Turkey and Turkey being a popular tourist destination for Russian holidaymakers.
Read MorePutin meets Hollande: France and Russia getting closer
While trade sanctions were possible, Fordham didn't expect relations to worsen further, however: "Diplomatic meetings have been suspended, and some trade sanctions are possible, but we do not expect disruptions to energy ties at this point," she said in a note Wednesday.
John Bates, Portfolio Manager at Pinebridge, told CNBC that the relationship between Turkey and Russia "is very deeply entrenched," pointing out that there are business links, such as Russian bank Sberbank owning Turkish bank DenizBank.
"I think the key economic drivers shouldn't change too much provided that the diplomatic and political forces don't do anything silly," he said.