Jamie Moore, 39, faces child endangerment charges, and authorities have accused the mother of physical abuse and neglect.
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Jashyah and the teen's 3-year-old brother have been removed from their mother's custody. An investigation is underway.
Before her disappearance, Jashyah Moore was last seen at a deli near her home in East Orange, New Jersey, on the morning of Oct. 14.
MORE: Reward increased, search continues for missing New Jersey teen Jashyah Moore
Nearly a month later, police located the 14-year-old in New York's Harlem neighborhood Thursday after a passerby recognized her and notified the police.
Jashyah spent the past month and a half in several New Jersey locations before ending up living in a Brooklyn shelter, Essex County Prosecutor Theodore Stephens said Friday.
Stephens said the teen had cut her hair and did not want to return home.
"It appears she was a runaway ... It appears she was more comfortable where she was," he said.
During the search for Jashyah, her mother denied that she had run away from home and claimed that her daughter was abducted.
Essex County increased the reward for information on Jashyah's whereabouts to $20,000 earlier this week, but Stephens said it had not yet been claimed.
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"This reminds us that the lives of little Black and little brown girls is just as important as everybody else's lives," Stephens said last week. "And we know that Gabby Petito, which is a very, very notorious case that was constantly in the news did yield results and information. So we are hoping that today's effort will also bring some information so we can find young Jashyah."
While the cases of missing white women have been given more focus and urgency, people of color are disappearing at disproportionate rates. Black people make up 35% of missing persons reports but only 13% of the US population, according to 2020 FBI data. Meanwhile, white people make up 54% of missing persons reports and 76% of the U.S. population.
CNN Wire contributed to this report.