Ramiro Delreal-Contreras was arraigned Friday and charged with capital murder in the death of Ava Zapata.
He pleaded not guilty and not guilty by reason of mental defect.
Child welfare officials started an investigation into Zapata's injuries after emergency responders received a call about a sick child on May 2.
Auburn police said Zapata died of blunt-force trauma injuries.
Chief Assistant District Attorney Kisha Abercrombie said prosecutors have not yet decided whether to seek the death penalty.
The Opelika-Auburn News reports that a decision is expected soon.