The move to oust the Secret Service chief came in the wake of last week's arrest of a Chinese woman at Mar-a-Lago - President Trump's Florida retreat - who was found to have a host of cell phones and electronic devices.
"The Secret Service does not determine who is invited or welcome at Mar-a-Lago; this is the responsibility of the host entity," the Secret Service said in a statement.
Democrats in the Senate quickly demanded that Alles testify about the incident, and whether it was at all related to his departure.
As for Secretary Nielsen, earlier in the day, Nielsen spoke briefly to reporters about her departure, praising President Trump and those who work at DHS.
She made no mention of any reasons for her sudden departure decision.
Democrats in Congress raised their eyebrows immediately about the latest personnel moves at the Department of Homeland Security, noting the number of "Acting" officials at FEMA and other DHS agencies.
“The purge of senior leadership at the Department of Homeland Security is unprecedented and a threat to our national security,” said Sen. Diane Feinstein (D-CA).
Some Republicans also expressed concern about the departures from DHS.
“I am concerned with a growing leadership void within the department tasked with addressing some of the most significant problems facing the nation," said Sen. Ron Johnson (R-WI).
There were also reports that the head of legal immigration services (USCIS) might be in jeopardy - but conservative backers of the President were appealing to save the job of Lee Francis Cissna.
"This would not be "cleaning house", it would be burning the house down," tweeted illegal immigration critic Mark Krikorian, who has expressed his support for keeping Cissna.