The Russian agriculture watchdog, Rosselkhoznadzor, said in a statement that authorisations for five Ecuadoran exporters were suspended from Tuesday due to the detection of pests.
Nine out of 10 bananas imported by Russia come from Ecuador, according to Russian media.
The restrictions on certain flower imports will come into force on Friday. Ecuador is one of the world's top exporters of flowers, mainly roses.
The decisions come in the wake of Ecuadoran President Daniel Noboa's announcement on January 10 that he had accepted a US offer to exchange the Soviet-era equipment for modern US weapons in a $200 million deal.
The United States has said that the Ecuadoran equipment would be shipped to Ukraine to help Kyiv in its conflict with Russia.
The deal has angered Moscow, with foreign ministry spokeswoman Maria Zakharova saying last week that Ecuador had made a "reckless decision under serious pressure from external interested parties".
Zakharova added that Ecuador had a contractual obligation to not transfer such equipment to a third party without Russia's consent.
Noboa has said that Quito had every right to conduct the deal because it involved "scrap".
The Ecuadoran leader spoke with Ukrainian counterpart Volodymyr Zelensky during the swearing-in of Argentina's new President Javier Milei in Buenos Aires.
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