Manafort served Trump's campaign for almost five months, joining in March 2016 and climbing to be campaign chairman before stepping down in August 2016 after reports of his connections to pro-Russian forces in Ukraine.
Judge Ellis addressed Manafort's complaints about location by ordering his transfer to an Alexandria prison.
It's not clear yet whether or not Manafort will get the same perks in the new facility, but Ellis assured Manafort's legal team that the staff at the Alexandria Detention Center was "very familiar with housing high-profile defendants including foreign and domestic terrorists, spies and traitors".
In earlier court filings, Mr. Manafort's attorney said the distance of Northern Neck jail - two hours from Washington, D.C. - has made it hard to adequately prepare for trial.
Donald Trump's former campaign chairman had requested that his trial for bank fraud be pushed back to the fall because he's not able to adequately prepare from jail in Warsaw, Virginia.
Wednesday's special counsel filing also reveals that Mueller's team has been recording calls from Manafort's private phone, and are now using Manafort's own words against him.
Manafort's trial in Alexandria is scheduled to start July 25.
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In their court filing today, prosecutors sought to pick apart Manafort's arguments that he needs to delay the trial because of his jail conditions.
Furthermore, prosecutors said Mr. Manafort has his own bathroom and shower, a self-contained living unit - instead of a cell - that is larger than other inmates' space and he is not required to wear a prison uniform.
Manafort's will now be housed in an Alexandria, Virginia facility. Visitors' logs show Manafort having multiple visits each week with his lawyers, according to the prosecutors.
Judge Ellis denied Manafort's bid to stay put at the jail he is now residing at and ordered him to be moved to the Alexandria Detention Center.
Defense lawyers, in response, said the government had selected "snippets" of the conversations to support their version of events. They said Mueller's team "does not pause to consider the reasons a detained defendant might have to make his situation sound better when speaking with concerned friends and family".
Attorneys for Manafort also took issue with prosecutors' revelation of the content of some of Manafort's personal phone calls and suggested that Manafort was sugar-coating his conditions of confinement to ease the concern of friends and family.