Mr. Trump had tolerated the seemingly endless drips of scandal surrounding Mr. Zinke in part because he liked him personally and in part because his focus on the cabinet was concentrated on his desire to oust Mr. Sessions.

At the same time, though, Mr. Trump disliked the bad press that was amassing for Mr. Zinke, given how it reflected on him personally. And as the incoming House Democratic majority made clear that Mr. Zinke would be a prime target, Mr. Trump’s aides convinced him that the time had come to shove out Mr. Zinke.

A few months ago, the White House Counsel’s Office indicated to some West Wing aides that officials would be less likely to be subpoenaed by the new House majority if they left before the new Congress was sworn in in January. That has helped speed up the departures of several.

“This is no kind of victory, but I’m hopeful that it is a genuine turning of the page,” said Representative Raúl M. Grijalva, who as the incoming chairman of the House Natural Resources Committee has repeatedly tangled with Mr. Zinke. He added, “The next interior secretary should respect the American people’s desire for strong environmental standards and an end to corporate favoritism.”

Mr. Zinke’s exit follows that of the other major architect of the Trump administration’s environmental policies, Scott Pruitt, the administrator of the Environmental Protection Agency. Mr. Pruitt, also known for his aggressive rollback of environmental regulations, resigned in July amid questions about alleged spending abuses, first-class travel and cozy relationships with lobbyists. Among other actions, Mr. Pruitt came under fire for reaching out to the chief executive of Chick-fil-A with the intent of helping his wife open a franchise.

Beyond examining the real estate deal, the Interior Department’s inspector general had faulted Mr. Zinke for allowing his wife, Lola, to travel in government vehicles, contrary to department policy, and chided him for using $12,000 in taxpayer money to take a charter plane after a talk to a hockey team owned by one of his biggest donors.

The inspector general has also been examining the secretary’s decision to block two Native American tribes from opening a casino in Connecticut after his office received heavy lobbying from MGM Resorts International. The entertainment giant had been planning its own casino not far from the proposed tribal one.