A 36-year-old man was busted for manslaughter in the death of his girlfriend’s 3-year-old son in the Bronx, cops said on Saturday.

Police found Messiah Allen unconscious inside the Bruckner Boulevard apartment that suspected killer Kenneth Lynch, 36, shared with his girlfriend at Sotomayor Houses in Soundview around 11:30 p.m. Friday.

The toddler was discovered with broken teeth and bruises all over his face and body, police sources said. Messiah’s mother was at work at the time of the incident.

Lynch called 911 and frantically performed CPR before authorities arrived, cops said. The boy was rushed to Jacobi Hospital, where he was pronounced dead. Police ruled the death a homicide.

During initial questioning, Lynch claimed to cops that the boy was injured when he fell out of his stroller last week.

Lynch was arrested late Friday and charged with manslaughter. His arraignment was pending Saturday morning.

The family has a history with the city’s child welfare agency from a few years ago, but the case did not involve physical abuse, according to a source.