Speaking ahead of the launch of Whole Foods' healthy eating initiative - which will train staff to advise on nutrition - Mackey admitted his shelves were laden with fatty products.
Mackey told the Wall Street Journal: "Basically, we used to think it was enough just to sell healthy food, but we know it is not enough. We sell all kinds of candy. We sell a bunch of junk. We've decided if Whole Foods doesn't take a leadership role in educating people about a healthy diet, who the heck is going to do it?"
The store's new promotion will also encourage staff to practice what they preach, with employees to be given bigger store discounts if they meet targets to lose weight, stop smoking or reduce cholesterol or blood pressure.
Mackey said from the autumn the stores will rid themselves of unhealthy food, and will try to educate customers with in-store promotions. He said: "There will be someone in a kiosk to answer questions, they'll have cookbooks and health books, there will be some cooking classes. It will be about how to select food, because people don't know."
Mackey's comments have put his UK division, which was already on the defensive following a Food Standards Agency report last week , on the back foot.
Some UK papers are calling Mackey's comments his Gerald Ratner moment, after the former chief executive of jewellery retailer Ratner Group who damaged his company's reputation in a 1991 speech jokingly describing its products as "crap".
But Jeff Tunas, head of UK operations at Whole Foods, has claimed Mackey's words had been lost in translation and he simply meant that too many crisps and cakes, even if organic, are still not healthy. Whole Foods owns five UK stores, all in London.