Margaret Morris, 57, the former finance director of St. Patrick's Seminary and University has been accused of embezzling more than $200,000 and stealing a donated Mercedes Benz.
Morris has been charged with four counts of felony theft and one count of swindling more than $65,000 worth of property.
Along with Morris, the San Mateo County District Attorney's Office also charged her secretary, Evelyn D. Vallacqua, 44, who helped issue several improper reimbursement checks to her boss and accepted unauthorized severance payment from the seminary.
Vallacqua has been charged with three counts of felony embezzlement
Morris's preliminary hearing has been scheduled for April 12. She has pleaded not guilty and is out of jail on a $200,000 bail.
Vallacqua is also out on a $10,000 bail and her first appearance in court is scheduled on April 30.
The university officials learnt about the missing seminary funds when they conducted an audit and discovered that over a six-year period starting 2006 Morris had been using her personal credit card to make work purchases, even though she was given a credit card for seminary needs, and accumulated airline miles.
Morris worked as a director of finance, beginning 2004 and supervised Vallacqua.
The audit uncovered that Morris reportedly made $166,000 worth of unauthorized personal purchases and overpaid herself by $36,000 in 2011-12.
District Attorney Steve Wagstaffe said that they were not sure where all the money went.
Meanwhile, Morris stole a 1982 Mercedes Benz that had been gifted to the college by registering the vehicle in her name while charging the registration and maintenance costs to the seminary.