The Kips Bay man accused of shaking his 6-month-old nephew to death in May is now facing heavier charges — manslaughter instead of just assault.

Luis Melendez, 33, remains held without bail for the May death of Alex Jose-Fernandez, his sister’s baby, at her home on Second Avenue near East 26th St.

Newly-completed autopsy reports resulted in the heightened charges, which accuse him of recklessly causing the baby’s death, officials said. Melendez now faces a potential maximum sentence of 15 years.

He’s due back in Manhattan Supreme Court on Oct. 26 for the chance to plead not guilty to the new indictment.