Binance and executives Gambaryan, a US citizen and head of financial crimes compliance, and British-Kenyan national Nadeem Anjarwalla, a regional manager for Africa, face four counts of tax evasion.
In a separate case, they have also been charged with laundering more than $35m and engaging in specialised financial activities without a licence. They have all pleaded not guilty to the money-laundering charges.
Binance's lawyer declined to comment after Friday's court hearing. Gambaryan's lawyer also had no comment.
"We are deeply disappointed that Tigran Gambaryan, who has no decision-making power in the company, continues to be detained," a Binance spokesperson said in a statement on Friday after the court hearing.
"These charges against him are completely meritless. He should be freed while discussions continue between Binance and Nigerian government officials."
Gambaryan remains in custody while Anjarwalla fled the country in March. Nigeria's security adviser's office has said it is working with Interpol to seek Anjarwalla's arrest.
The chief executive officer of Binance has accused Nigeria of setting a dangerous precedent after its executives were invited to the African country in February for talks with authorities and then detained as part of a crackdown on crypto.
Binance itself has not been charged in the tax-evasion case by Nigeria's Federal Inland Revenue Service (FIRS), which has said Gambaryan could face the charges on the exchange's behalf.
Gambaryan's lawyer has previously said Gambaryan was "neither a director, partner nor company secretary" and had no written instructions from Binance to face the charges on its behalf.
Judge Emeka Nwite ruled on Friday that Gambaryan should be served with the charges against Binance because he is the chief financial compliance officer of Binance and he was duly appointed to represent it in a meeting in Nigeria.
Gambaryan will be arraigned in court on Wednesday to take a plea on behalf of Binance.
Gambaryan's bail application in relation to the money-laundering case was denied on Friday.
Nigeria has blamed Binance for its currency woes after cryptocurrency websites emerged as platforms of choice for trading the Nigerian naira currency, as the country grappled with chronic dollar shortages.
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