A longtime Orange County murder suspect in the decades-old cold case of Megan McDonald is now behind bars, after a long-awaited indictment this week.

Edward Holley came to Orange County Court a free man on Friday, but left in handcuffs.

The Wawayanda man pleaded not guilty at his arraignment in Goshen after his indictment for second-degree murder, almost a year after his arrest in 2023.

Prosecutors said in court that Holley bludgeoned his ex-girlfriend, who was 20 years old, more than a dozen times in 2003 with a blunt object and left her body near a dumpster in the town of Wallkill.

Holley’s attorney, Paul Weber, tried to keep him out of jail but the judge disagreed with his arguments that Holley, who is paraplegic, requires specialized medical care that cannot be provided while incarcerated, and set bail.

“I’m pretty pissed off,” says Weber. “Holley is innocent. We are going to point out who the real suspects are.”

Emotions ran high during the appearance and Holley’s daughter stormed out of court.

State police said last April that new DNA evidence finally led them to solve the cold case, but the case has been riddled with problems since, and it was unclear – up until now – if the charges would even stick.

Orange County District Attorney Dave Hoovler scolded police for allegedly failing to notify his office of an arrest and stepped aside citing a conflict because he previously represented a person of interest in the case who is deceased.

Holley was arrested for his alleged role in McDonald’s death while he was incarcerated on an unrelated narcotic charge, according to authorities, and without an immediate indictment, he was let go after the completion of his sentence.

Special prosecutor Julia Cornachio was assigned to the case, and tasked with the daunting challenge of reviewing 20-years of evidence, it took 10 months to turn up an indictment.

Holley seemed unfazed in court but looked withdrawn when he was later seen in custody. It could now be months before the start of trial and his bail was set for $500,000.

If found guilty, Holley could face up to 25-years to life in prison.

He’s due back in court Feb. 21.