Morale sank lower last week when Mr. Baker said that Rebecca Blumenstein, a deputy editor in chief who had been at The Journal for 22 years, was leaving for The New York Times, where she will become one of the paper’s highest-ranking editors. The announcement surprised and saddened many in the newsroom, where Ms. Blumenstein had been viewed as a potential successor to Mr. Baker.

At Monday’s meeting, Mr. Baker answered questions about The Journal’s strategy going forward and acknowledged that the paper had to address concerns about diversity and offer more opportunities for women in the newsroom.

But the issue of covering Mr. Trump was front and center, after an episode two weeks ago when Mr. Baker sent a note instructing editors to avoid the phrase “seven majority Muslim countries” when writing about Mr. Trump’s executive order on immigration.

“It’s very loaded,” Mr. Baker wrote at the time. “The reason they’ve been chosen is not because they’re majority Muslim but because they’re on the list of countries Obama identified as countries of concern.”

Mr. Baker later sent a note to employees clarifying that there was “no ban on the phrase ‘Muslim-majority country’” but that the publication should “always be careful that this term is not offered as the only description of the countries covered under the ban.”

The discontent among a faction of journalists over coverage of Mr. Trump stretches back months, according to current and former employees. There was unease in the newsroom after Mr. Baker wrote a column in The Spectator, a conservative British magazine, about Mr. Trump’s victory. During the meeting on Monday, Mr. Baker, in answer to a question about the column, admitted that he probably should have resisted the temptation to write it, according to some of the people who participated.

The Journal’s coverage has also drawn criticism from outside. In late November, after Mr. Trump falsely claimed on Twitter that “millions of people” had voted illegally, the paper was derided online for printing a front-page headline that parroted Mr. Trump’s assertion without pointing out that it was inaccurate.