Popular grocery store chain Trader Joe’s Co. has agreed to spend an estimated $2 million over the next three years to reduce greenhouse gas emissions from refrigeration equipment at 453 of its stores, according to a court settlement reached Tuesday.

The privately held Monrovia-based chain will also pay a $500,000 civil penalty as part of the agreement with the U.S. Department of Justice and the Environmental Protection Agency to resolve alleged violations of the Clean Air Act.

“Today’s settlement will affect all of Trader Joe’s current and new stores to prevent the release of approximately 31,000 metric tons of carbon-equivalent greenhouse gases,” said Alexis Strauss, a regional administrator for the EPA.

Trader Joe’s allegedly violated the Clean Air Act by failing to promptly repair leaks of R-22, an ozone-depleting substance used as a coolant in refrigerators.

Trader Joe’s said it will achieve and maintain an annual corporate-wide average leak rate of 12.1 percent through 2019, which the Justice Department noted as being well below the grocery store sector average of 25 percent.

“The company-wide upgrades Trader Joe’s will make are not only good for the environment, they set a high bar for the grocery industry for detecting and fixing coolant leaks,” said Cynthia Giles, an assistant administrator for the EPA’s Office of Enforcement and Compliance Assurance.

The settlement is the third in a series of recent cases involving national grocery store refrigerant, including cases previously filed against Northern California’s Safeway Inc. and Costco Wholesale Corp.