Sewell announced her departure in a letter to the NYPD rank and file a couple of weeks ago.
She has not addressed publicly why she's leaving.
Mayor Eric Adams, who was seemingly taken by surprise by the announcement, has not named a reason either.
An NYPD promotions ceremony in College Point, Queens took an emotional turn Friday morning, as the department played a video tribute to the commissioner.
Sewell, who was seated onstage, wiped tears from her eyes as the video played.
She then received a standing ovation that lasted several minutes, the crowd ignoring her attempts to wave it off.
WATCH: Emotional tribute to outgoing NYPD Commissioner Keechant Sewell
The mayor's chief advisor, Dr. Chaplain Lewis-Martin, then called a line of administration officials, including all five female deputy mayors, to the stage.
One by one they said tearful goodbyes. It wrapped up with Sewell being presented a large bouquet of flowers.
"We thank you. No one could have done a better job. You broke the ceiling, and breaking the ceiling is never easy. And you did it. We love you!" said Lewis-Martin, adding "she didn't want to do a walkout, but we were determined that you would know and feel the love. We thank you."
Mayor Adams was not present at the ceremony but posted a final appreciation tweet.
"I am so proud and thankful for all the work Police Commissioner Keechant Sewell has done for our city. Since the beginning, she has been committed to making our communities safer while also supporting the brave men and women of the NYPD," Adams tweeted. "We've seen her hard work pay off in the reduction in crime and from New Yorkers who tell us how much safer they feel on our streets and in our subways. This was a 24/7/365 role, and we are all grateful for Commissioner Sewell's service to NYC."
Sources say tensions between the commissioner and the mayor had been brewing for some time now and that she has felt micromanaged by the mayor's team.
Sewell made history as the first woman to lead the NYPD, and she stepped in when the crime rate throughout the city was rising.
Mayor Adams has commended the work Sewell has done.
In the email she sent to the members of the NYPD, Sewell encouraged everyone to continue this work, writing in part: "There are people all over this city who want and appreciate you. They want safe streets, transit and housing. They are families, workers, tourists, business owners and students, and they depend on the NYPD. Please continue to do what you do well to secure this city."
"Commissioner Sewell carried out her role and she did it well. Look at the numbers, the numbers speak for themselves. You cannot lie when you see them. It was extremely brilliant to bring her on board, turn around morale, bring down crime. Really better involvement with our city." Adams said.
The mayor has declined to say who he's considering for the job, but it's likely First Deputy Police Commissioner Edward Caban who will be stepping in as interim commissioner.
This is the first time a Latino would be leading the NYPD.
As of now, it appears the commissioner's last public event will be overseeing a promotions ceremony in Queens later Friday morning.
Meanwhile, the Police Benevolent Association and the Detectives Endowment Association said Sewell's leadership and legacy wont be forgotten.
"This is a great loss, this is a really outstanding leader," Boyce said. "The men and women really respected her. And she carried herself with so much grace and discipline, and genuine sincerity."
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