In the wake of discovering they'd lost nearly half a million dollars to a trusted employee, leaders of the downtown Charleston homeless shelter said they will weather the storm.

Last week the nonprofit, now in its 30th year of operation, discovered their former chief financial officer, Carol Libby, allegedly stole $440,000 between 2006 and 2013, according to court records.

Federal charges were brought against Libby, 56, of Mount Pleasant on Tuesday in connection with the theft. She was charged with five counts of wire fraud.

Libby, who worked at the organization for 10 years, is accused of bilking four times the amount that Crisis Ministries originally believed had been stolen.

Libby was fired and arrested by Charleston police in June and charged with breach of trust.

At that time, investigators believed she'd stolen at least $96,000, according to authorities.

Recently filed court documents revealed the former CFO fraudulently generated more than 400 unauthorized business checks from Crisis Ministries over a period of seven years that she made payable to actual vendors, according to prosecutors.

Libby is accused of endorsing those checks by forging the names of the vendors and writing her bank account number on the backs of the checks, court records said.

She then deposited those checks into her account, according to court records.

Libby, however, continued paying the vendors through the organization's account, according to Executive Director Stacey Denaux.

"It was very deceitful. She understood how our vendors do business. She knew if a vendor wasn't paid, there would be a phone call," Denaux said. "It was a very well thought out, methodical deception."

The group has retrieved about half the amount they lost, according to Denaux.

Donors have contributed $150,000 since Libby's arrest, designated specifically to offset the loss. The organization's insurance has paid it $50,000 and Libby has paid Crisis Ministries $52,000 in restitution so far, according to Denaux.

"I think it's fair to say we're still pursuing all avenues available to us to recoup these funds," said Board Chairman Paul Kohlheim.

So far, Libby has been cooperating with prosecutors, according to Assistant U.S. Attorney Rhett DeHart.

It is unclear what sentence Libby would face if convicted. Prosecutors declined to comment on the matter.

Libby's attorney, Bill Runyon, said there have been substantial efforts by his client to rectify any shortages of money by Crisis Ministries.

Runyon would not comment further on the charges or details about the case.

"She is, of course, extremely upset by this whole situation and extremely remorseful, but this isn't the appropriate time for us to be making statements," he said.

Crisis Ministries has been working with law enforcement since Libby's arrest to discover the extent of the alleged theft. A financial audit was conducted and delivered to the nonprofit last week.

The shelter's programs and services have not been compromised since the discovery, according to Denaux.

"It was very slow, relatively small, individual transactions over a long period of time," Denaux said.

In the past seven years, the time period in which Libby was accused of stealing money, the organization's annual budget grew from $2 million to $7 million annually, according to the group's leaders.

"Unfortunately, that success became an opportunity for someone who was aware of that growth," Denaux said.

Denaux said she doesn't want to trivialize the amount of money stolen, about 1 percent of their budget over the past seven years.

"It's still a significant amount of money," she said. "But percentage-wise, that's what made it easy to hide."

Kohlheim said the organization had the appropriate safeguards in place but called Libby's approach a sophisticated manipulation of their financial data. Since her arrest, the board has implemented strengthened financial controls, including having third parties review financial transactions.

Denaux said they continue their commitment to assist the community's homeless population, including the completion of the shelter's new facility on Meeting Street, which would double its size. "Homelessness didn't stop because someone committed a horrible crime and thankfully people recognize that," she said.

Earlier this month, the organization asked for the public's help to raise $1.5 million needed to complete the $7.7 million project.

Crisis Ministries' leaders hope the community continues to support their efforts to provide the homeless shelter, food and other services. "We run a very good organization and appropriately controlled organization," Kohlheim said. "We just got taken advantage of."

Reach Natalie Caula Hauff at 937-5594 or Twitter.com/ncaula.