The city will move to close three charter schools at the end of this school year, including one that helped start New York’s charter movement, officials said Friday.

Citing poor academic performance and unmet goals, the city said it would not renew the charters of Beginning with Children Charter School in Brooklyn, Lefferts Gardens Charter School in Brooklyn, and Staten Island Community Charter School. The announcement marks the start of the second round of charter school closures under Mayor de Blasio, who has said school closures should be a last resort.

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“Each of these schools were given clear conditions with benchmarks for performance, and they failed to meet them,” Chancellor Carmen Fariña said in a statement.

The three schools, all authorized by the city Department of Education, have struggled. City officials pointed out that Lefferts Gardens, an elementary school, has had three principals in three years and saw its students’ passing rates on the state English exams fall last year to 11 percent, compared to its district average of 22 percent.

Staten Island Community also saw its English pass rates dip, to 19 percent, compared to an average of 30 percent across the city and 35 percent in Staten Island.

Beginning with Children has had the highest-profile decline. The school opened in Williamsburg at the urging of philanthropists Joseph and Carol Reich in 1992 with many of the freedoms now associated with charter schools, before charter schools were even legal in the state. It became an official charter school in 2001, retaining its unionized teachers and operating with help from a foundation with the same name.

But a dispute over that teachers union contract led the foundation to withdraw support in 2013, and the school’s board of trustees then voted to voluntarily dissolve the school. New board members were soon elected and spent the next few years trying to right the ship. Still, the share of its students passing the state math and English tests declined last year, and district averages are twice as high.

Leaders of the three schools did not immediately respond to messages on Friday.

The city’s announcement does not mean the schools are certain to close, as charter schools have successfully fought attempts to shut them down before.

Last spring, Fariña announced plans to close Brooklyn’s Fahari Academy Charter School, which remained open this school year. Other city charter schools, including Peninsula Prep and Williamsburg Charter High School, won earlier legal fights to keep their doors open.

But James Merriman, CEO of the New York City Charter Center, signaled that the schools might not get continued support from the rest of the charter sector, which has encouraged the closure of poor-performing schools to maintain its reputation as intolerant of academic mediocrity.

“Nobody wants to see a school closed, but it’s important that authorizers maintain high standards and hold charters accountable,” Merriman said.