Chicago Housing Authority CEO Eugene Jones Jr. abruptly resigned Tuesday, ending a highly acclaimed, 4.5-year run that brought stability to an agency that sorely needed it and compassion to public housing residents.

“He was a great leader...He had a great relationship with the residents. Every time you turned around, it was not unusual to see Gene at an event the residents were organizing. Whether it was a summer picnic, the Christmas holiday party or Thanksgiving dinner, he was there,” said Ald. Pat Dowell (3rd), chairman of the City Council’s Budget Committee.

“What you see is what you get with Gene. He always kept them updated about what was going on at the CHA. And he was visible. That’s like the main thing. He didn’t just sit in his office downtown.”

City Hall sources said the decision to step down more than a year before his $291,500-a-year contract expired was made by Jones alone. He was not pushed out the door by Mayor Lori Lightfoot. To the contrary. The mayor wanted him to stay.

“I want to thank her for the opportunity to stay on and serve CHA’s residents and to be a part of the larger efforts to help build and strengthen our neighborhoods. I also want to thank our Board of Commissioners for their continued confidence in me,” Jones was quoted as saying in an emailed statement.

Jones, whose resignation takes effect on Sept. 27, said he has worked hard to meet the CHA goal to produce more housing and expand “housing opportunities” in every neighborhood.

“From bringing new investment to communities and forming innovative partnerships that led to the development of three co-located housing and libraries, the development of new community assets like grocery stores and recreational facilities and the settlement earlier this year of the landmark Gautreaux case, I leave knowing that the CHA is well-positioned for the future and is prepared to meet the housing needs of its residents and the communities across our city,” he said.

The Gautreaux case is a 52-year-old lawsuit alleging racial discrimination in the way public housing was located in Chicago.

Lightfoot, on vacation, issued a short statement thanking Jones for his service. The mayor said a nationwide search for Jones’ replacement “will begin immediately.”

The decision to leave comes just five months after Jones stood before a City Club audience and shot down speculation that he was on his way out the door and headed for New York City.

At the time, media reports out of New York had placed Jones on a short list of contenders to run that city’s housing authority. Some stories had identified Jones as the front-runner.

That job has since been filled. A spokesman for Jones did not know his plans, other than that he will “pursue other opportunities.”

At that City Club event, Jones had said: “I’ve not interviewed for a job. I’ve not talked to anyone for a job. … It’s an honor for someone to even think about going to run the largest housing authority in North America. That’s fine and dandy. But I have made my commitment to CHA, to my residents, to my staff and also to my board.”

With a new mayor expected to make wholesale changes at city departments and public agencies, Jones joked openly on that day about having talked to CHA Board chairman John Hooker about his uncertain status.

“I said, ‘John, three companies are after me. What should I do? Look at, maybe an increase in salary. So we sat down. We started talking. He finagled. We discussed it. And he said, ‘OK, Gene. 5 percent.’ I said, ‘OK,’” Jones said.

“As I was leaving his office, he says, ‘Gene, I want to ask you. Who were the three companies?’ I said, `The gas, the cable and the electric companies.’”

In 2015, Jones left the Toronto Community Housing Corporation under a cloud after a scathing report by that city’s ombudsman, and arrived at the CHA, becoming its fifth CEO in four years.

Jones had resigned the Toronto job “by mutual agreement” — with a $200,000 severance package — after being accused of exercising an “abject failure of leadership” and creating a “climate of fear” at an agency that had shelled out $1.6 million in severance in 2013.

Toronto City Ombudsman Fiona Crean said Jones and his leadership team flouted rules governing hiring and firing, ignored conflicts of interest, gave managers sudden and unjustified raises and “recklessly” fired underlings.

In Chicago, those controversies were washed away by Jones’ energetic performance to finally get, as now former Mayor Rahm Emanuel put it, “close to delivering” the long-stalled Plan for Transformation promised by former Mayor Richard M. Daley when CHA high-rises were dismantled.

In December, a settlement was reached to resolve the Gautreaux case.

The CHA and Business and Professional People in the Public Interest, which represents the plaintiffs in the case, hammered out a “detailed road map” to complete the requirements for CHA to “offset the impacts of racial segregation caused by its historic building and tenant assignment practices.”

Their goal is to close the Gautreaux case by July 31, 2024.

In March, Emanuel introduced Jones to the City Club and sent a clear signal to his successor that, even if there’s a housecleaning, Jones should be a keeper.

“The old way of doing work was just counting units built. But housing without a library, housing without a grocery store, housing without a transportation center is an island of housing isolated from a neighborhood,” the mayor said then.

“The legacy that Gene has built at CHA is to re-invent, re-imagine what a housing authority can be. It is not, by itself, just counting housing units — whether it’s Section 8 vouchers or how many units you build. But when you put those units around with all the other pillars that build a neighborhood, then you build something where the residents that rely on public housing become part of a community where they can raise their kids.”