Jake and Rebecca Haro — the parents of missing 7-month-old baby Emmanuel Haro — have pleaded not guilty to murder.

The controversial couple — who authorities believe are responsible for the disappearance and death of little Emmanuel — arrived at the Riverside, California courthouse separately Thursday to be formally charged with murder and filing a false police report.

Both Jake and Rebecca pleaded not guilty to murder with malice Thursday. They’re held on $1 million bond each … their next hearing is scheduled for Sept. 16.

The Haro case has captured the nation’s attention due to its many twists and turns. Rebecca initially reported their son missing on Aug. 14, telling reporters Emmanuel was snatched from a parking lot in Yucaipa, about an hour and a half east of Los Angeles.

Rebecca said she was changing Emmanuel’s diaper next to her car in the parking lot when someone approached her, punched her in the face, and took off with the baby.

However, investigators found inconsistencies in Rebecca’s story … prompting a K9 search of the Haro family home and the seizure of Jake’s car for evidence.

The couple then stopped cooperating with the authorities when Jake’s past willful child cruelty conviction came to light.

On Aug. 22, authorities arrested Jake and Rebecca for murder … with Riverside County District Attorney Mike Hestrin alleging in a press conference that Emmanuel was a victim of extended abuse — and that he likely succumbed to his injuries. Hestrin said in last week’s presser investigators have a “strong indication where the remains of Baby Emmanuel are.”

Emmanuel’s remains have yet to be recovered, however.

San Bernardino County Sheriff Shannon Dicus said there was “some level of cooperation with the suspects involved” when asked about Jake having been spotted in a jumpsuit and shackles on the side of a freeway accompanying investigators during an unsuccessful search for the child on Aug. 24.