While the filing in the Manafort case, which focused on lies the former campaign manager told following his guilty plea with the special counsel's office, did not seem to make any references to Trump, separate court filings by the special counsel's office in Cohen's case, and by New York Southern District prosecutors, make several references to "Individual-1", who is the president.
The explosive revelation came a week after Mueller said that Cohen had detailed to the Russian Federation collusion investigation ongoing contacts with a top aide to Putin on the real estate deal throughout the first half of 2016, even after Trump had secured the Republican presidential nomination.
Last week, Cohen admitted to lying to congressional investigators in an attempt to minimize his efforts to secure the Kremlin's help for a Trump skyscraper in Moscow.
The filing from Southern District of NY prosecutors alleges that Trump ordered Cohen to make hush money payments to two women who said they had affairs with Trump, a fact revealed some time ago.
In a separate filing, Mueller's office said on Friday that it would not take a position on Cohen's sentencing, scheduled for next Wednesday. White House spokeswoman Sarah Sanders called Cohen a liar and dismissed the filings as insignificant.
In new tweets on Friday, Trump accused federal investigators and senior officials of having conflicts of interest, without offering evidence.
Cohen said he was directed by "Individual-1", who is believed to be Trump, to make payments related to the rights of the stories from two women who claimed to have had affairs with Trump.
There is "no bigger warranty in any project than consent of (the president of Russia)", the person told Cohen.
Trump says his campaign had nothing to do with them and he denounces Mueller's investigation as a "hoax" and a "witch hunt".
However, in the crimes to which he pleaded guilty in August, he was motivated "by personal greed and repeatedly used his power and influence for deceptive ends".
Cohen has pleaded guilty to lying to Congress about negotiations between Trump's business and powerful Russians about a prospective Trump Tower in Moscow, a building that ultimately was never built.
They said Cohen should receive some credit for his cooperation with Mueller, but noted that he had not entered into a cooperation agreement with their office.
The filings followed a sentencing memo earlier this week regarding Trump's former national security adviser, Michael Flynn, who Mueller praised for providing "substantial" cooperation and argued for no prison time.