A flagship program that recruits and trains 20 percent of New York City’s new teachers each year will soon be under new management.

Since it launched in 2000, the NYC Teaching Fellows program, which quickly trains career changers and recent college graduates to fill hard-to-staff positions, has been run in part by the nonprofit TNTP.

Now, the city education department is planning to kill its $4 million-a-year contract with TNTP when it expires in February. Instead, the department will manage the program itself.

It’s unclear exactly why the city chose this moment to end the contract with TNTP. City officials said the organization has effectively run the fellowship program’s day-to-day operations, and said the change was not a cost-saving measure. But it continues the education department’s trend under Chancellor Carmen Fariña of taking more control of, and interest in, professional development and training.

“The contract is ending, we evaluated our options, and we now have the capacity to do this work — and build on it — in-house,” education department spokesman Will Mantell wrote in an email.

Born out of a shortage of certified teachers, the fellowship program was conceived to quickly place professionals from other fields into the city’s classrooms, skirting the traditional certification process.

It has since become a key pipeline for filling positions in the Bronx and in subjects like math, science, and special education — and has helped attract a more racially representative group of teachers to the field. In a typical year, the program sends roughly 1,200 teachers into city classrooms, and about 10 percent of the city’s current teaching force came through the program.

Shael Polakow-Suransky, who served as a deputy schools chancellor under Mayor Bloomberg, said the Teaching Fellows program has for years filled critical vacancies and brought talented teachers into the system, but also raised questions about teacher quality and retention.

“Maybe what we are seeing is the beginning of some shifts to address those issues,” he said.

And while the program is widely seen as a key recruitment tool, it also has a powerful detractor. Just months after Mayor Bill de Blasio took office, the city’s teachers union pressed him to cancel its contract with TNTP. It’s unclear if that lobbying continued, or had any impact on the city’s decision, but the union cheered the move not to extend the contract.

“We applaud the DOE for saving the taxpayers money and moving the program in-house,” United Federation of Teachers chief Michael Mulgrew said in a statement. “For years TNTP has managed to make money from the Department of Education by recruiting teachers who would have come here anyway.”

Teaching fellows receive about two months of intensive training before they start working in classrooms full-time, where they simultaneously earn a master’s degree and complete certification requirements. (The traditional pathway typically involves at least a year of training, including a student teaching stint.)

Until now, TNTP has managed significant parts of that training and recruitment.

“This is a bittersweet moment for us, because we value our involvement in NYC Teaching Fellows enormously,” Dan Weisberg, TNTP’s CEO, said in a statement. “But we’re always pleased when our district partners feel ready to take the reins of these kinds of programs, and we agree the time is right for the city to do that here.”

Education department officials said they did not have plans to downsize the program or significantly change its structure.

“We’re deeply committed to the NYC Teaching Fellows program as a pipeline to recruit and train high-quality teachers for our students, and this administration has expanded and strengthened the program,” Amy Way, the education department’s head of teacher recruitment and quality, said in a statement.

The decision follows a similar plan to move training for aspiring principals in-house. In June, the city ended the NYC Leadership Academy’s involvement in that training program.