A 3-month-old boy died shortly after his mom woke to find him unconscious in her bed inside their Bronx apartment Saturday night, police sources said.

Alexondra Ambrosini, 32, was sleeping with her son, Mark Ruane Jr., at their Ogden Avenue home when she awoke at around 11:30 p.m. and discovered he was unresponsive, sources said.

She called 911, and the infant was rushed to Bronx Lebanon Hospital but couldn’t be saved, police said.

Police and the city’s Administration for Children’s Services are investigating the death.

The child-welfare agency has been involved with the family before. Ambrosini and her partner, Mark Lodger Ruane, 35, had their older son, Emerald, taken away for nine months after he was born in 2015 because the parents tested positive for drugs, according to court documents.

“[The] respondent parents use illicit substances, including cocaine, benzodiazepines and marijuana and fail to participate in a drug treatment program,” the family court found.

Both parents were on methadone at the time, and Ambrosini was receiving mental-health treatment, according to court papers.

The parents subsequently sued the agency and the social workers who said the baby was in “imminent danger,” claiming the drug allegations were falsified.\

The legal battle is still ongoing. Last month, Ruane filed a letter requesting a new court date, saying he couple had split up and that he was busy moving out of their apartment, court documents show.

In a Facebook post around the same time, he suggested that the kids were in danger living with Ambrosini and espoused on his apparent dislike of “Child Protective Services.”

“I hate CPS, I don’t wanna call them but she won’t communicate and assure me my kids are safe after I read an email from her mom to her dad saying she almost killed my two month old,” he wrote.

When the couple did live together, they regularly engaged in screaming matches, and the baby was often crying, according to neighbors who declined to give their names.

Five years ago, Ruane didn’t have a home at all. The Army veteran was profiled in a 2012 story, living and panhandling on West 32nd Street as he struggled to get help from Veterans Affairs for his bipolar disorder.

ACS would not comment on either child’s case.

“We are involved in an active investigation along with the NYPD on this matter. Confidentiality laws preclude us from commenting further. We await the medical examiner’s review,” a spokesman said.