The head of Crisis Ministries said the alleged embezzlement of about $96,000 by one of her employees was a betrayal but vows that the homeless shelter will survive.

“It’s hit us all to the core,” Stacey Denaux, the nonprofit’s chief executive officer, said. “Our administrative office has nine people in it. We’re very close, so it was a personal and professional betrayal like I don’t think any of us have ever felt.”

Carol Libby, who served as the homeless shelter chief financial officer for the past 10 years, was charged with breach of trust on Thursday. A magistrate judge set her bail at $25,000 during an afternoon hearing.

Libby, 55, of Royal Links Drive in Mount Pleasant, is accused of stealing $96,199 — far more than an original estimate of $11,000, according to an arrest affidavit from the Charleston Police Department.

Between Dec. 13, 2011, and June 3, Libby took checks from the nonprofit and made them payable to “various vendors,” the document stated. She then deposited the checks into her own bank account and used the money for personal expenses, according to the affidavit. Her attorney, Bill Runyon, told a reporter after the hearing that Libby was an “outstanding employee.”

“This came as a total shock to everyone,” he said. “The entire family is distressed over the allegations.”

Libby moved to Charleston from New York to escape cold weather and has an accounting degree from the State University of New York, Runyon said. She’s been married for more than 15 years and has a 14-year-old daughter, the attorney said.

Her husband appeared during the bond hearing, but he did not say anything to Magistrate Linda Lombard. Because of the amount Libby is accused of stealing, the charge she faces is a felony punishable by up to 10 years in prison. She also could face a fine determined by the court. Libby does not have a previous arrest history.

Runyon said he could not comment on Libby’s personal financial situation or discuss the allegation.

“It’s too early to be saying anything,” he said. “Everyone has questions that frankly we don’t have the answers to quite yet.”

The accusations and controversy surrounding the allegations seemed surreal to Denaux even a week after the discovery of the missing funds. While she spoke to a reporter on Thursday afternoon at the shelter, she called Libby’s alleged crime an unbelievable act. “I’m still having conversations thinking I’m watching this, like this isn’t really happening right now,” she said. An initial incident report from the Charleston Police Department stated that Libby had cashed 10 checks, but the scope of the alleged embezzlement broadened after the nonprofit’s officials first learned of the missing money a week ago.

Denaux said she got a call from their bank on June 6 to alert her that checks had been deposited into a personal account. She informed the chairman of the Crisis Ministries board and then called police, she said. Since then, the organization hired an independent auditor to examine its financial records. Denaux said the cost of that audit is unknown at this time.

Libby was suspended without pay pending the investigation’s outcome. Crisis Ministries also hired an independent contractor to serve as chief financial officer to perform the daily fiscal operations, Denaux said.

“We still have to pay our bills. We still have to make payroll. We still have to raise money,” she said.

Despite any pending costs for the audit and the missing funds, which the nonprofit hopes to recover, Denaux said the organization will survive.

“This does not define our organization. We will be stronger,” she said. “The organization is in a very strong financial position, even with this hit. That’s not to say we don’t still need donations. We live by the gifts people give us.”

Outside the Meeting Street homeless shelter on Thursday, work on an expansion continued as construction crews installed earthquake drains into the ground below the future 30,000-square-foot facility, which will house the men’s shelter and soup kitchen.

It’s supposed to be completed next summer and Denaux said this doesn’t change that.

“Our clinical team is assuring those living here they don’t have to worry about where they’ll sleep tonight,” she said. “We’re not going anywhere.”

Reach Natalie Caula at 937-5594 or Andrew Knapp at 937-5414.