Although the charges have nothing to do with Mueller's primary goal of investigating Russian interference in the 2016 US presidential election including possible collusion with the Trump campaign, the stakes are extremely high for both the president and the special counsel.
"Evidence or argument relating to Mr. Manafort's work for then-candidate Trump's campaign in 2016 or the Special Counsel's investigation of the campaign's alleged collusion with the Russian government is wholly irrelevant to whether Mr. Manafort's personal income tax returns were false, whether he willfully failed to file reports of foreign accounts, and whether he conspired to commit, or committed, bank fraud", defense lawyers wrote.
That task comes as the president and his lawyer-spokesman, Rudy Giuliani, have intensified their attempts to undermine the Mueller investigation in the court of public opinion and as the president continues to waffle on whether he'll sit for a private interview with prosecutors.
If the judge rules in their favour, prosecutors could present evidence that delves deeper into Manafort's Russian connections. Manafort would eventually help Viktor Yanukovych, the leader of the Russia-aligned Party of Regions, win the presidency in 2010.
Manafort is charged with lying on tax forms and bank fraud.
Gates, former national security adviser Michael Flynn and George Papadopoulos, a foreign policy adviser on the campaign, all have pleaded guilty.
Manafort had been under federal investigation since 2014 over suspicion of illegal lobbying and financial improprieties.
Ellis has since ruled that Mueller is acting within the scope of his investigation in pursuing charges against Manafort.
The heart of the government's case involves nine years of Manafort's lucrative lobbying and consulting for Ukraine and its former leader Victor Yanukovych, work the USA government said Manafort should have registered with the Justice Department.
When Yanukovych fled to Russia, Manafort and his business partner Richard Gates experienced a severe cash crunch, and the men allegedly began leveraging real estate to take out new loans, providing false or incomplete profit and loss statements and other data to banks. So far, 32 people and three companies have been charged by Mr Mueller.
According to former prosecutors, Gates' agreement with Mueller will likely be a target of Manafort's attorneys when they get a chance to cross examine him.
The judge overseeing that trial, Berman Jackson, revoked Manafort's bail last month and ordered him to await trial from a jail cell.
He faces two criminal trials, the first in Alexandria, Virginia, and another later in Washington. Witnesses have been told to avoid any mention of President Trump or anything related to his 2016 campaign.
Manafort, a veteran Republican political consultant, served as chairman of Trump's presidential election campaign for three months in 2016 before being forced to step down amid questions about his lobbying work in Ukraine.
However, prosecutors say - the focus will be on Manfort's links with Ukraine, not on collusion with Russian Federation.
"You really don't care about Mr. Manafort's bank fraud.What you really care about is what information Mr. Manafort could give you that would reflect on Mr. Trump of lead to his prosecution or impeachment", Ellis said.
Up until the the day before Mueller unveiled Gates' plea deal, there were contradicting reports on whether he would actually flip.