D'Amico and McClure said they were rationing the money to keep Bobbitt from using it on "something stupid".
McClure has been charged with theft by deception and conspiracy.
Bobbitt was arrested on Wednesday night by in Philadelphia and remains in custody. McClure and D'Amico have already turned themselves in.
The viral story that warmed hearts around the world went like this: Bobbitt, a homeless Marine vet, gave McClure his last $20 after she ran out of gas. He said that he'd received around $US75,000 ($103,126) but the rest was being withheld.
But with questions looming about how much - if any - of the money was left for Bobbitt, a judge ordered that the couple appear before the court for a deposition.
They denied wrongdoing. Their lawyer did not answer a phone call.
Bobbitt's lawyer says he has been told the money is gone.
A Philadelphia prisons spokeswoman says Johnny Bobbitt was brought in Wednesday night by USA marshals and remained in custody Thursday on probation detainers and a $50,000 bond.
Police raided McClure and D'Amico's New Jersey home in September, taking bags and boxes of items and the BMW the couple had purchased.
D'Amico has said Bobbitt spent $25,000 in less than two weeks in December on drugs, in addition to paying overdue legal bills and sending money to his family. Inspired by his kindness, she and her boyfriend, D'Amico, set out to raise $US10,000 ($13,750), allegedly to get him on his feet.
GoFundMe and the law firm representing Bobbitt issued a joint statement last week saying he would receive all the money raised for him.
Burlington County Prosecutor Scott Coffina is planning a news conference Thursday afternoon.
"Every dollar he ever touched was used for drugs", Mr D'Amico told NBC in a nationally televised interview in August.
Investigators say the couple hid elements of their fundraising page in order to conceal information "that would affect their judgment about solicited contribution to that fundraising effort". Others believed Bobbitt was being robbed by an unscrupulous couple. GoFundMe always fully protects donors, which is why we have a comprehensive refund policy in place. The exact timeline for that isn't clear but will be "in the coming days" ahead. He later filed a lawsuit against McClure and D'Amico.
Finally, it's important to understand that misuse is very rare on our platform.
"Campaigns with misuse make up less than one-tenth of 1% of all campaigns", he said. "It's simply standard policy to remove fraudulent campaigns from the platform", Whithorne says.