Trump had told his acting chief of staff Mick Mulvaney tofire Alles two weeks ago, marking the latest top official to be forced out of their position during the tumultuous administration.
Alles had been in the role for two years and came into the job after serving time as a major general in the Marines.
The departures indicate unstable circumstances at the Department of Homeland Security, which oversees the Secret Service.
More firings or departures may be coming in the coming weeks, as the dust settles from Nielsen's abrupt resignation. Alles reported to Nielsen.
Multiple senior administration officials tell CNN that POTUS told chief of staff Mick Mulvaney to fire US Secret Service director Randolph “Tex” Alles, a conversation that took place a week before last. Alles remains in the position as of now but has been asked to leave.
An administration official said the decision to seek Alles' resignation was made two weeks ago - before a March 28 incident in which a Chinese woman was arrested at Mar-a-Lago without an invite, sparking security concerns, NBC reported.
"This was not based on any single event," the official said.
Alles had been told Trump was preparing to make changes in leadership throughout the Department of Homeland Security, which includes oversight of the Secret Service.