The superintendent who helped steer contentious school integration plans for Manhattan’s District 3 is leaving her post for a position in the education department’s central office.

Ilene Altschul will step down Monday as leader of the district that spans the Upper West Side and part of Harlem. She will take on a new role helping districts improve how they serve students who need extra support, such as those with disabilities, the education department announced on Friday.

Her departure means that it will be up to new leadership to see through the district’s fledgling efforts to better integrate District 3 middle schools. That plan came on the heels of an elementary school rezoning, which was driven partly by a desire for more diversity but sparked intense pushback from some parents. 

The education department named as acting superintendent Christine Loughlin, who had served as a deputy superintendent on Staten Island.

Last June, District 3 became the first to win approval for changes to the way students are assigned to middle schools, giving some students who have struggled in school or come from low-income families priority for admission. Families in the district must apply to schools, which are allowed to select students based on measures like attendance or report card grades. The hope is that admissions changes will help shift demographics, since performance on standardized tests is often linked to race and class.

In a statement, Altschul said she was “particularly proud” of ushering through the middle school changes, “which will benefit students for years to come.” 

This was the first year the admissions changes were in place. Advocates have warned that it is still a work in progress, with much to be done to support schools that may need to adapt to serving different populations of students. Now schools need equal resources to attract more families and make up for the negative consequences of segregation, and parents need more information so they’ll consider a broader range of options for their children. 

“I think she deserves a lot of credit for doing as much as she did, but of course it’s difficult,” said Kim Watkins, the president of the district’s Community Education Council, of Altschul. “Of course there were times we disagreed with her.”

Altschul helped navigate the changes through sometimes extreme pushback from parents. She also felt heat from members of the district’s Community Education Council, who at times argued the superintendent fell short of engaging and informing Harlem families on such issues as school closings or mergers, or having concrete plans to lift up schools in that part of the district.

Genisha Metcalf, an advocate for Harlem schools who previously served as a member of the district’s Community Education Council, said she was often frustrated that the district’s integration work didn’t focus more specifically on the needs of the schools that were struggling most. But she also said that many of the challenges faced in Harlem are more systemic than any district superintendent’s office could fix, and questioned whether a change of leadership would make much of a difference.

“I’m just unclear how this is better or different than what we were experiencing,” she said. “If you don’t get the community you’re working with, then it’s hard for you to get the job done.” 

Loughlin comes from one of the city’s whitest and wealthiest school districts. The education department said she has been overseeing Staten Island’s work on a state grant that provides funding and support for local districts that are devising their own integration plans. 

“I will work closely with school leaders and the community as we emphasize instruction and learning across the district and implement the District 3 middle school diversity plan,” Loughlin said in a statement. “I look forward to rolling up my sleeves and meeting with students, families, principals, teachers and staff.”

She previously served as principal at the Henry Street School in Manhattan, and as a social studies teacher and assistant principal at the Michael J. Petrides School.

A spokeswoman for the education department said the city will kick off the process this fall to find a permanent leader.