His reaction was, "Of course it happened this way", one person said. "But there's not a plan locked in place at this point".
McGahn could not be reached for comment.
While the Times presented McGahn's cooperation as "unusual", Trump tweeted that it was all a part of the unprecedented level of transparency his administration has had with regards to the Russian Federation investigation.
But Mr McGahn was well-liked in Washington DC, with Senate Judiciary Chair Chuck Grassley lamenting his departure. Additionally, whoever takes over his position will likey have their hands full, dealing with the Special Counsel's possible subpoena of the President to testify before a Grand Jury and hand over documents, should Democrats win the House and decide to impeach.
After the news of McGahn's conversations with Mueller went public, Trump tweeted that McGahn was not a "RAT" like John Dean in the Watergate scandal.
In a sharply worded tweet earlier this month, Mr Trump said he had allowed Mr McGahn to give testimony to the special counsel. Other Trump advisors have suggested aggressive response to Mueller's probe, but McGahn has quietly advocated for stasis. "It is no surprise to read that he has gained the president's confidence already", Coffin said.
These discussions reportedly touched on Trump's firing of FBI Director James Comey and his focus on putting loyal officials in charge of the investigation, such as Attorney General Jeff Sessions. Flynn pleaded guilty in December 2017 to lying to the Federal Bureau of Investigation.
The development comes as legal risks to the President rise, following the conviction of his former campaign chairman Paul Manafort last week on fraud charges and his former personal lawyer Michael Cohen's guilty plea to charges of fraud and campaign finance violations.
McGahn's exit also continues the churn of staffers as the administration sets records for turnover and the White House struggles to fill key vacancies.