Manafort "made multiple false statements to the FBI, the OSC and the grand jury concerning matters that were material to the investigation," including his contacts with his Russian associate during the campaign and later, Judge Amy Berman Jackson wrote on Wednesday.
Manafort was convicted of various financial crimes in August, and then cut the deal to plead guilty to two charges of conspiracy and witness tampering in September.
In all, Jackson determined Manafort intentionally lied about $125,000 he received for the legal bills, about another unnamed Justice Department criminal investigation and about his interactions with his longtime Russian associate Konstantin Kilimnik while he was campaign chairman and later.
Jackson noted twice in her order that two of the topics Paul Manafort lied about, Kilimnik and payments he received for his legal bills were "material to the investigation."
Manafort is still bound by what he agreed to in the plea, so he will not be able to retract his guilty pleas. But the finding frees Mueller's office from its contractual obligations in the plea, like asking for a reduced sentence for him because of his cooperation.
Mueller spokesman Peter Carr declined to comment.
Manafort's lawyers have maintained that he did not intentionally lie.
The judge reviewed extensive transcripts and evidence that would give her a window into Mueller's work, and her ruling shows that Manafort's lies were serious enough to disrupt his cooperation.
Jackson said the special counsel's office did not fully show that he had "intentionally made false statements" on two fronts where prosecutors alleged he lied: about his interactions with White House officials or about Kilimnik's role in an attempt to influence witnesses, which Manafort admitted to doing in his plea.
Prosecutors have said they don't have plans at this time to bring additional charges against Manafort. But the finding Wednesday that Manafort misled prosecutors brings additional detractions into his upcoming sentencings. He will ultimately receive two sentences that could total decades in prison, one for the financial convictions and one for the guilty plea.
Jackson is scheduled to deliver the first sentence on March 13. Manafort has been in jail for eight months already.
The two judges who will sentence Manafort will weigh, among other things, whether he has accepted responsibility for his actions.
Prosecutors and the defense team hashed out what happened in Manafort's interviews at a four-and-a-half hour sealed court hearing last week, then again in a closed hour-and-45 minute hearing Wednesday afternoon.
During the first sealed hearing, prosecutors described an August 2, 2016, meeting Manafort had with Kilimnik, according to a transcript released later. At that 2016 meeting, prosecutors and the defense team conflict over whether then-campaign chairman Manafort discussed a plan with Kilimnik about Ukrainian peace, which could have had ramifications on US sanctions against Russia. Some of the contact Mueller and news outlets have exposed since 2016 between Russians and Trump campaign officials have focused on sanctions, like the Trump Tower meeting in June 2016 with campaign leaders and Michael Flynn's calls with then-Russian ambassador Sergey Kislyak.