How do I categorize Amazon FBA fees, storage fees, and referral fees in my books?
The biggest mistake Amazon sellers make is dumping every fee into a single “Amazon Fees” expense account. Your settlement report might show $4,000 in total fees, but that tells you nothing about which fees are growing, which products are expensive to fulfill, or whether your advertising is actually paying off. You need separate accounts to see where your margin is going.
Here is how to break it down. Create individual expense accounts (or sub-accounts under a parent “Amazon Fees” account) for each major fee category.
Referral Fees are the percentage Amazon takes on every sale, typically 8% to 15% depending on category. This is essentially your cost of selling on the platform. Track it separately because it scales directly with revenue and varies by product category.
FBA Fulfillment Fees cover the per-unit pick, pack, and ship costs Amazon charges. These vary by product size and weight. If fulfillment fees are eating into a particular product’s margin, you need to see that clearly so you can decide whether to adjust pricing, change packaging dimensions, or consider merchant fulfillment for that item.
Storage Fees include both monthly storage and long-term storage fees. Monthly storage is based on cubic feet of space your inventory occupies. Long-term storage fees kick in for inventory sitting 181 days or more and can be significant. Tracking this separately helps you identify slow-moving products that are costing you money just to sit in a warehouse.
Advertising Fees are your PPC spend through Amazon Sponsored Products, Sponsored Brands, and other ad types. This should absolutely be its own account. Mixing advertising costs with platform fees makes it impossible to calculate your true advertising cost of sale (ACoS) or evaluate whether your campaigns are profitable.
Other Fees is a catch-all for removal orders, disposal fees, labeling fees, and any other miscellaneous charges. These tend to be smaller but can add up if you’re frequently removing or relabeling inventory.
In QuickBooks, you can set these up as sub-accounts under a parent “Amazon Marketplace Fees” account. This gives you a clean view on your profit and loss statement. You can see total Amazon fees at a glance but also drill into each category. When you review your e-commerce financials monthly, you will immediately spot if storage fees jumped because inventory is sitting too long or if fulfillment costs increased because of a size tier reclassification.
The settlement reports Amazon provides every two weeks contain all of this detail. The data is there. It just needs to be mapped to the right accounts consistently. If you have months or years of everything lumped together, working with bookkeepers in Orlando who understand Amazon seller accounting can help you restructure your chart of accounts and reclassify historical transactions so your reporting is actually useful going forward.
Getting this right turns your books from a tax compliance requirement into something that helps you make better sourcing, pricing, and inventory decisions every month.
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