He is due to make a second court appearance later Wednesday in Virginia where he faces a separate indictment.
U.S. District Court Judge Amy Berman Jackson set Manafort's trial date for September 17.
Following Gates' guilty plea, Mueller's office moved to drop charges from the Virginia indictment. The very next day, Manafort's associate Rick Gates, himself charged under the new indictment as well, capitulated to special counsel Robert Mueller's team and made a plea deal, citing family concerns as one of his reasons.
In the statement last week, Manafort said: "I had hoped and expected my business colleague would have had the strength to continue the battle to prove our innocence". She said if it happened again, she would issue an order to show cause as to why the order had not been violated. He was originally indicted a year ago with Gates, Trump's former deputy campaign manager.
The allegations stem from much of the same conduct outlined in the Washington case, and prosecutors attempted to have all the charges brought in the pending case there.
The political impact is hard to predict, but it could aid Democrats eager to keep the focus on what US intelligence officials have warned will be a renewed Russian effort to meddle in the USA campaign this fall.
Gates and Manafort are accused of preparing false tax returns, Bank fraud, conspiracy to commit Bank fraud, money laundering, disclosure of income from foreign sources, the conspiracy against the interests of the United States and the misrepresentation of the American authorities.
Manafort has pleaded not guilty to all the charges he faces, although numerous legal observers say he is under increasing pressure to strike a deal with prosecutors.
"I can certainly understand the impulse to not let that go by without asserting your innocence", Jackson told Manafort, referring to Gates' plea and "hundreds" of news articles about it.
"Right now, the order stands", Jackson said.
"I think the burden is going to fall heaviest on the defense" for trial preparations, she said.
The loans, which Manafort received in December 2016 and January 2017, were previously examined by Mueller's team, but no connection was found between them and the Russian Federation probe at that time.