HAYWARD -- AC Transit's chief financial officer appeared in Alameda County Superior Court on Wednesday morning and entered a not guilty plea to charges he embezzled more than $500,000 from one of Oakland's largest churches.

Lewis Clinton Jr., 57, faces four counts of grand theft with white-collar enhancements after prosecutors say he embezzled money from the Allen Temple Baptist Church from 2007 through 2013.

Clinton was accompanied by his wife and his attorney, Michael Thorman, at the Hayward Hall of Justice.

After Clinton entered his plea, Judge Scott Patton ordered a conditional exam in the case, which would allow some of the witnesses' testimony to be taped and replayed at trial, if necessary. Such exams are used when witnesses are elderly, ill or unable to attend a trial.

Lewis Green Clinton Jr., AC Transit’s chief financial officer, at the Hayward Hall of Justice, May 21, 2014. (Anda Chu/Bay Area News Group)
Lewis Green Clinton Jr., AC Transit's chief financial officer, at the Hayward Hall of Justice, May 21, 2014. (Anda Chu/Bay Area News Group)

The judge set the exam for Wednesday and a subsequent pretrial hearing for early July.

Clinton remained silent as he held his wife's hand while exiting the courtroom. He is a parishioner at the 5,000-member church and served on three overlapping volunteer boards that administered hundreds of thousands of dollars meant to provide housing and help for low- and moderate-income residents.

Officials believe he used the money that he allegedly embezzled to pay for a luxury car, private schooling for his children, mortgage payments and a golf club membership, according to court documents.

Allen Temple Baptist Church officials have said through attorney Jessica K. Nall that they are cooperating in the ongoing investigation and prosecution.

Clinton, who had a warrant issued for his arrest after the charges were filed, was arraigned last month on the felony charges.

The judge set his bail at $100,000, which Clinton posted shortly afterward, a court clerk said.

AC Transit spokesman Clarence Johnson said Clinton was placed on indefinite paid administrative leave on April 14. He said that he was not aware of any connection between the district attorney's investigation and the transit agency's finances.

His colleagues last month expressed surprise at the charges but said the transit agency's ongoing financial audits made it very unlikely that any public funds could have been taken.

Johnson previously said that during the six years he's worked with the agency, they've had no complaints filed against Clinton, whom he called a competent and trusted employee.

The agency's finances are audited at least three times a year, he said -- twice by the Federal Transit Administration and once by an outside firm. The most recent audit took place in November, Johnson said.

Clinton was preparing to put together a new budget for the agency when he was charged, AC Transit board President Greg Harper said. When asked if the agency will now audit the financial transactions Clinton was involved in, Harper said it's a possibility.

Chris Peeples, who has served on the AC Transit board for the past 16 years, described Clinton as a "smart guy" who previously worked as a Wall Street investment banker.

"Being in the finance business for a long time, he has a level of financial sophistication that we previously lacked," Peeples said. "We are all concerned and watching this with a great level of interest."

Contact Natalie Neysa Alund at 510-293-2469. Follow her at Twitter.com/nataliealund.