He wrote: "How can FBI Deputy Director Andrew McCabe, the man in charge, along with leakin' James Comey, of the Phony Hillary Clinton investigation (including her 33,000 illegally deleted emails) be given $700,000 for wife's campaign by Clinton Puppets during investigation?"
Trump's tweets also rehashed an alleged controversy surrounding 2016 campaign donations made by Virginia Gov. Terry McAuliffe, an ally of Hillary and Bill Clinton, to McCabe's wife, who was running for (and eventually lost) a seat in Virginia's Senate.
The letters come as Mueller's team is facing heightened scrutiny in recent weeks following reports that two FBI officials who would later be assigned to the special counsel's investigation called Trump an "idiot" and "loathsome human" in a series of text messages a year ago.
The FBI has said McCabe did not start overseeing the Clinton investigation until his wife's state Senate campaign was over.
Allies of the president have seized on the messages and other details about Mueller's team to allege it is biased against Trump.
Like Comey, Trump also reacted to the news of McCabe's retirement on Twitter, but he predictably chose to attack the deputy director for supposedly trying to take advantage of his retirement benefits and for having previously accepted money from the Clintons.More news: 'Real Housewives' star Luann de Lesseps arrested in Palm Beach
It's disappointing", he said, "to see how the criticism of the FBI is being used to try to undermine the credibility of the Mueller investigation.
"FBI Deputy Director Andrew McCabe is racing the clock to retire with full benefits", Trump tweeted at 3:30 p.m. Mr. McCabe was deputy director when the F.B.I. opened the investigation in July 2016.
Trump's frequent and blistering attacks on the nation's premier law enforcement agency have proven a tough challenge for Wray, who took the reins in August after Trump fired James Comey as he was leading the bureau's probe into possible Trump campaign ties to Russian Federation during the 2016 presidential election.
McCabe has come under fire from Republicans over the past year because of the bureau's investigation into the Clinton email issue as well as the probe into possible collusion between Trump's 2016 presidential campaign and Russian Federation.
President Trump has been critical of McCabe for months, blasting him as a "Comey friend".
Congressional Republicans had called for McCabe's ouster earlier in the week in light of the release of an anti-Trump text message sent by an Federal Bureau of Investigation agent supposedly connected to the deputy director.