Fifty-six-year-old Carol Libby of Mount Pleasant is accused of taking the money from Crisis Ministry between 2006 and 2013.
The former chief financial officer of the ministry has been charged in federal court with five counts of wire fraud.
Libby was fired last June after she was arrested by Charleston police and charged with breach of trust. She had worked for the organization for 10 years.
Officials thought last summer she had taken about $96,000.
Executive Director Stacey Denaux says the organization has recovered about half of the amount that was taken. Donors have offered $150,000 and insurance has paid $50,000. Denaux says Libby has repaid $52,000.