The operators of Whole Foods Markets will pay nearly $800,000 to settle allegations of overcharging customers at California stores, the Los Angeles City Attorney’s Office announced Tuesday.

The settlement follows a yearlong investigation involving county and state Weights and Measures officials who determined that the Austin, Texas, chain’s customers paid more than the advertised price for goods, according to City Attorney Mike Feuer. The investigation determined that the weight of containers wasn’t deducted when customers paid for self-serve items, packaged items that were sold by the pound had less food than reported on the label and deli items were sold by the piece instead of by the pound.

Whole Foods cooperated with the investigation. Spokesman Michael Silverman wrote in an email that the retailer’s equipment was accurate 98 percent of the time and that the company has strengthened its pricing policies for weighed and measured goods.

“While we realize that human error is always possible, we will continue to refine and implement additional processes to minimize such errors going forward,” Silverman wrote.

City attorneys representing Santa Monica and San Diego joined Los Angeles in the settlement, according to Feuer’s office. The agreement covers all 74 Whole Foods stores operating in California. Ten of those are in Los Angeles.

The five-year agreement requires Whole Foods to appoint two coordinators to ensure pricing accuracy at all California stores, assign an employee at each store to check for accurate prices and conduct four price audits per year at all stores.

Whole Foods Market stock fell slightly Tuesday to close at $38.95 on the Nasdaq.