McCabe, who served as acting Federal Bureau of Investigation chief for more than two months previous year after Trump fired agency director James Comey, had been expected to leave his post as the No. 2 FBI official in March.
Earlier this month, reports surfaced that Attorney General Jeff Sessions pressured FBI Director Christopher Wray to push McCabe out, and the Washington Post reported that Trump, after firing former FBI Director James Comey, asked McCabe how he voted in the 2016 election.
An FBI spokeswoman declined to comment on McCabe.
McCabe has become a lightning rod in the political battles surrounding special counsel Robert S. Mueller III's probe into whether any Trump associates co-ordinated with Russian agents to interfere in the 2016 presidential race.
As expected he will take accumulated leave and remain on the payroll until March when he is eligible to retire with full benefits. The president and some congressional Republicans accused him of bias.
The inspector general is also looking into whether Comey made improper decisions, including his decision to announce the FBI would not recommend charges and his subsequent decision to publicly announce he was re-opening the investigation just 11 days before the 2016 election, after new emails were discovered.
But a source familiar with the matter said FBI Director Christopher Wray told McCabe he is bringing in his own team, which he would not be a part of, and that it was McCabe's decision whether to stay at the FBI or leave. These donations all occurred before McCabe took over as deputy director of the FBI and before he would have had any oversight into the Clinton email investigation.
In tweets and in private, Trump fumed that McCabe was partial to Hillary Clinton because of campaign donations his wife received from Clinton allies during an unsuccessful Virginia state senate run in 2015. Jill McCabe had recently lost her bid for a state Senate seat.
During the call, Trump suggested that McCabe ask his wife how it feels to be a loser, in an apparent reference to her failed campaign for office, according to NBC.
A career civil servant who had served at the Federal Bureau of Investigation since 1996, McCabe has been at the center of ongoing tensions between the law enforcement agency and Republicans.
"The president was not part of this decision-making process", she said.