Can i use my amazon prime in the store for discounts or do i need to order it delivered?

You can use Amazon Prime in store. You have to download the Whole Foods App on your phone and link your Amazon Prime account. Then when you go to check out, open the App and it’ll show your unique QR code. Hold that under the scanner which is hidden on the back of their stand where they scan your items (you should see a picture of a QR code where it’s located).

I haven't tried to do that...