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Whole Foods Market claims several energy efficient initiatives on the store website, including installing electric vehicle charging stations, harnessing solar energy, achieving green building certificates, using green refrigeration, and designing grocery stores of the future.

In 2006 Whole Foods Market was amongst the first retailers, and the first Fortune 500 company, to offset 100% of their emissions by purchasing Renewable Energy Credits (RECs). Skepticism surrounding this purchase and RECs as a whole have been prevalent online. Harvard Business Review writes that “the money paid to purchase those RECs, in theory, subsidizes the higher cost of producing clean electricity, making this alternative competitive, or creates a market mechanism that will cause more renewables to be produced.” The energy produced by wind farms that are benefactors of RECs is distributed to the same power grid as energy from fossil fuels, making the success of RECs difficult to track and quantify. Energy policy researcher Michael Gillenwater states that “claims that the U.S. green power market result in additional wind power lack credibility.” A 2022 study found that the purchasing of RECs inflates the actual value of this environmental commodity in terms of limiting emissions.

Whole Foods Market also has several stores that function entirely on UTC power fuel cells on-site. One of the company's Mississippi locations plans on utilizing a local wind farm funded by Amazon to source the store’s energy needs. In the case study of a Raleigh, North Carolina Whole Foods Market, the company worked with the U.S. Department of Energy’s Commercial Building Partnerships to plan and evaluate the construction of an extremely energy-efficient building, which if successful, would have been rolled out to other locations. Whole Foods Market is also working with the Environmental Protection Agency's GreenChill program to reduce refrigerant emissions. Refrigeration is extremely energy-intensive, leading the company to start using a refrigerant with a 68% lower global warming potential than the most commonly used refrigerants.

Whole Foods signed an agreement with SolarCity to install solar panels on up to 100 stores. In 2015 the company was named in the top 25 companies by number of solar installations. Whole Foods also reduced their energy usage by 21% between 2010 and 2021.

Whole Foods Market extends their energy initiatives globally. The company’s non-profit organization, Whole Planet, which aims to alleviate poverty also pertains to climate mitigation. In 2023 the company announced that they would fund the distribution of solar home kits across Sierra Leone, making energy more accessible with a Pay-as-you-Go model.