Whole Foods Market deductions: the complete guide

Whole Foods Market (Amazon-owned) is a retailer, not a distributor like KeHE or UNFI — which changes how deductions work. Instead of a distributor passing retailer chargebacks through a shared portal, you invoice Whole Foods directly per purchase order under its pay-by-PO program, and deductions are taken against those invoices.

When a payment comes in lower than your invoice — from an invalid chargeback, a pricing discrepancy, or a short-pay — you dispute it through the Whole Foods supplier portal under Resources → Payment Dispute. The process is documented, but it's manual: an Excel template plus a Smartsheet form, and it's limited to suppliers on the pay-by-PO program.

The principles you already know from distributor deductions apply here: disputes are won on documentation (PO, invoice, delivery proof, agreed pricing), and acting promptly matters because retailers generally operate on tighter, less published windows than the 180-day window a distributor like KeHE publishes.