It was McCarthy's first court appearance since his December 18 indictment. He's scheduled to be back in court February 16.
The girl's mother, Rachelle Bond, 40, is charged as an accessory to murder after the fact. She has also pleaded not guilty.
Prosecutors say McCarthy thought Bella was possessed by a demon and killed her, either by suffocating, or as Bond has claimed, by repeatedly "punching her in the stomach until she stopped breathing."
Bella's body was found in a bag June 25 on a Deer Island shoreline in the Boston Harbor. The mystery of the unknown child -- who became known as "Baby Doe" -- captivated the nation for nearly three months.
A computer-generated image made by police to help garner tips was shared on social media by more than 50 million people. One of those tips came from Michael Sprinsky, a longtime friend of McCarthy, who ultimately helped put a name to the mystery girl.
Prosecutors revealed new details of their case on Monday.
David Deakin, an assistant district attorney, said Bond told investigators that McCarthy said he would kill her or have her killed if she told anyone what she had seen on the night Bella died. McCarthy then allegedly wrapped girl in a garbage bag and put her body in a refrigerator.
Then, according to Deakin, the two defendants went on a two or three-day drug binge, while deciding how to dispose of Bella's body.
McCarthy allegedly picked up some weights from his father's plumbing business in Quincy and placed them in a duffel bag along with Bella's body. The two allegedly drove to the harbor and threw her over a seawall.
McCarthy's lawyer Jonathan Shapiro called the account "unbelievable," saying his client didn't murder the girl and that her mother was the culprit.
Back in October, a report by the state Office of the Child Advocate said the Massachusetts Department of Children and Families failed to properly investigate child abuse claims in Bella's case.
The report cited Bella's mother's previous history with child services in saying DCF prematurely closed the child's case in 2013.
Bond previously had two children taken away from her between 2006 and 2011. One was placed in the custody of a grandmother and another was adopted by an unrelated family. Bond also has a lengthy rap sheet of arrests, substance abuse, mental health issues and instability, according to the report.