The Los Angeles city attorney's office said Tuesday that the company had settled with three California cities: Los Angeles, San Diego and Santa Monica.
The probe found several problems with the company's pricing. In some instances, for example, the grocery failed to deduct the weight of containers when ringing up food from the fresh-food bars.
"By adding the weight of containers and packaging, especially on higher-priced, per-pound items like seafood and meats and even prepared food, the extra charges can add up fast, and yet be hidden from consumers," Santa Monica Deputy City Atty. Adam Radinsky said in a statement.
In other cases, the company gave customers less food than the weight stated on the label.
In the settlement, which applies to 74 Whole Foods outlets in California, the grocer agreed to random audits of its stores and to commit to accurate pricing.
"Based on a review of our own records and a sampling of inspection reports from various city and county inspectors throughout California, our pricing on weighed and measured items was accurate 98 percent of the time," Whole Foods said in a statement. "While we realize that human error is always possible, we will continue to refine and implement additional processes to minimize such errors going forward."