A Manhattan judge let one of the two men accused of plotting to attack New York City synagogues continue to walk free Wednesday — after prosecutors asked for the second time in two weeks that he be held in jail without bail.

Assistant District Attorney Edward Burns argued that disturbing new facts in the case of Matthew Mahrer, 22, were reason enough to keep him locked up after his family paid $150,000 in bail to set him free on Nov. 21.

“We now know that Mahrer, [accused accomplice Christopher] Brown and [a] third individual, drove to Pennsylvania on November 18 to purchase a firearm. That individual who drove with them has since been arrested by federal authorities,” Burns said. 

Prior to his arrest on Nov. 19, Mahrer had been sending an unnamed jailbird payments for the gun he and Brown planned to use in the would-be attacks last month, the prosecutor said.

Burns added that Mahrer has continued to financially support the incarcerated person — who was locked up for 3 1/2 years for criminal possession of a weapon — even after his own arrest.

He also told the judge that the troubled Upper West Sider — who has bipolar disorder and autism, according to his lawyer— had bought a bulletproof vest before he and Brown were busted carrying weapons and a Nazi armband linked to the alleged plot.

But defense attorney Brandon Lamour Freycinet fired back that that information was already known when Mahrer’s bail was previously set on Nov. 20.

After his release from jail, Maher was sent to Elmhurst hospital for roughly a week before returning to his family’s home on the Upper West Side. He has also enrolled in a group treatment called Pathways.

Manhattan Supreme Court Justice Neil Ross sided with the defense, but warned that Mahrer must continue to appear in court — or his family will be forced to forfeit the bail money they already paid. 

“Make sure you understand that this is the most important obligation that you’ve had in your life,” the judge warned.

Mahrer was later seen casually puffing a vape pen — and smirking — as he strolled free with his lawyer in Lower Manhattan. He declined to comment.

The FBI and NYPD had been on the trail of Mahrer and Brown, a “diagnosed schizophrenic” who recently told family members that he wanted to go to New York and buy a gun, sources have said.

Cops seized a loaded handgun with an extended magazine and a bulletproof vest from Mahrer’s Upper West Side apartment that he and a buddy allegedly planned to use in a synagogue attack, according to prosecutors.

Outside the courthouse, District Attorney Alvin Bragg held a press conference about why his office twice asked that the suspect be remanded.

“We requested a remand at the initial arraignment. We requested it today based on the seriousness of the facts when we made our application,” he said, adding. “The judge ruled.”

He added that it was “important” to note that Brown had been held without bail last month.

Brown also appeared in court Wednesday, in handcuffs, as both he and Mahrer were arraigned on indictments charging them in the alleged plot.

Police last month seized a loaded handgun with an extended magazine and a bulletproof vest that Mahrer and Brown allegedly planned to use in a synagogue attack, prosecutors said.

Both were hit with a slew of charges, including counts of conspiracy, criminal possession of a weapon and criminal possession of a firearm. Brown also faces terrorism and hate crime charges.