During the testimony, Manafort did not stare Gates down as he did on Monday.
The high-powered political consultant is facing 18 counts and a maximum 305-year prison sentence if the Eastern Virginia jury finds him guilty.
Accountant Cindy LaPorta - who was granted immunity from prosecution - said on Friday she suspected that Gates was misleading her about Mr Manafort's finances.
When his consulting work dried up after the change of power in Ukraine, prosecutors say Manafort turned to using loans.
Prosecutors on Monday went through a list of overseas corporations and Gates testified that all of them were controlled by Manafort and contained income earned by his political consulting work.
Laporta detailed multiple examples in which Manafort and Gates sought to doctor financial records - first to lower Manafort's taxable income and then later to inflate his income so that he could get bank loans, she said. But there are plenty more details that were laid out in the indictment against Manafort that Gates hasn't yet discussed that will likely be raised on Tuesday.
Not once did he let his eyes wander to the defense table, where Manafort sat, arms crossed, staring at his former protégé as he testified against him.
But Mr Manafort is not charged with helping the Kremlin.
The charges largely predate Manafort's five months on the Trump campaign but were the first to go to trial arising from the special counsel Robert Mueller's investigation into Russian interference in the 2016 United States election.
What did Gates tell the court? This is just the first of two trials in cases based on allegations involving Manafort and Gates.
Special counsel Robert Mueller's team indicated it expects to question Gates for three more hours on Tuesday before the defense team will get its chance to grill him.
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That second part is true - kind of.
He added that he had stolen "several hundred thousand" dollars from Mr Manafort by submitting false expense reports.
That's but a drop in the ocean of the roughly $30 million prosecutors are claiming Manafort hid from the IRS. The funds were logged as loans, but Gates testified they were in fact compensation to Manafort.
When the trial broke for lunch Tuesday, Manafort looked back at his wife, sitting in the front row, smiled and winked at her, followed by a quick shake of his head, seeming to indicate he was unfazed or unbothered by the morning's testimony. But while Laporta acknowledged that she regularly communicated with Gates, she said she believed Manafort was in the know.
Gates didn't respond to any of her emails asking for documents, contracts, and other communications about the alleged forthcoming payment.
The charges relate to Manafort's work for Ukraine's former pro-Kremlin president, Viktor Yanukovich. Ellis overruled the objection. But she noted that she couldn't imagine a scenario where she would have learned Gates was doing that.
But she said she was under the impression that Mr Manafort had been directing his deputies' actions and "knew what was going on".
So far, that testimony has provided jurors with a damning account. It is unclear what other information he may have provided to Mueller's team. He also admitted to concealing millions of dollars in foreign bank accounts on Manafortâs behalf.
In cross-examining Liss, one of Manafort's lawyers, Thomas Zehnle, argued that Manafort was required to file FBARs for his companies only if he owned more than 50 percent of them.
Prosecutors summoned Gates, described by witnesses as Manafort's "right-hand man", to give jurors the first-hand account of a co-conspirator they say helped Manafort carry out an elaborate offshore tax-evasion and bank fraud scheme.
When they appeared, the bookkeeper and accountants said, they thought the companies were clients or, in some cases, lenders.