Amazon FBA and FBM: bookkeeping, fees and reconciliation

Amazon FBA and FBM differ in fulfilment, but both require sales, fees, refunds and payouts to be reconciled. Accounting needs the underlying transactions and documents. A payout alone does not explain its components.

This guide complements Amazon accounting with KudTax, explaining which records to review for FBA and FBM and how to prepare a complete settlement period.

Amazon FBA bookkeeping: which additional records matter?

With FBA, Amazon handles storage and fulfilment. Your accounting process therefore needs fulfilment charges, storage costs and inventory movements. A storage charge cannot necessarily be assigned to an individual order like a referral fee. Review period-based statements as well. Amazon explains the fulfilment models and services.

For your monthly reconciliation, establish which sales and refunds were settled, which FBA costs have supporting records and which inventory movements need a separate review. This matters particularly when stock is held in several countries. The fulfilment model alone does not determine VAT treatment.

Amazon FBM bookkeeping: include your own fulfilment records

With FBM, you ship yourself or use a service provider. Amazon sales, referral fees, refunds and payouts still need reconciliation. Shipping, packaging and external storage costs may also come from your own supplier invoices.

Distinguish shipping amounts paid by customers from the invoice issued by your parcel carrier. They are different transactions; equal amounts do not make one record redundant. Also check whether shipping labels purchased through Amazon are already included in the settlement so that costs are not counted twice.

Example: FBA and FBM in one seller account

In a simplified settlement period, you collect €2,000 from customers, refund €100 and have €300 in fees withheld. With no other movements, the payout is €1,600. A separately paid €80 parcel carrier invoice for FBM is not an additional difference within this Amazon payout. It is another document in your overall process. This example describes cash movements, not tax treatment or account allocation.

If you use FBA and FBM together, keep the fulfilment method as an analysis field where your data provides it. Reconcile the combined payout first, then review cost allocation. Use existing order and settlement references rather than merging two unchecked sales lists.

Check	FBA	FBM
Amazon sales and refunds	Match settlements and documents	Match settlements and documents
Fulfilment costs	Check Amazon records	Add your carrier/service provider records
Inventory movements	Include Amazon inventory reports	Review your warehouse/service provider records
Shared payout	Include all underlying movements	Prevent duplicate sales or costs

Why an Amazon payout can differ from revenue

A single sale breaks into several events that appear at different times and in different reports. The payout is only the net result of all of them.

Data stream	Where it comes from	What it contains	Where it belongs in the books
Orders	order report	gross revenue, tax rate, destination country, shipping	revenue accounts, split by tax rate and country
Fees	settlement report	referral fee, FBA fulfilment, storage, advertising	expense accounts, ideally per order
Refunds	settlement report	returns, partial refunds, goodwill	revenue reduction plus proportional fee correction
Payouts	settlement report	the amount that actually moves	clearing account, never directly as revenue

An agreed clearing-account process connects the transactions with the payout. A remaining balance is not automatically an error: it may reflect pending payouts or reserves. What matters is being able to explain and document it.

How a single settlement report is taken apart line by line is covered in the post on Amazon settlement reports.

From order to journal entry

The sequence is the same every month, whether you have 100 orders or 100,000:

1. Pull order data — with tax rate, destination country and shipping per line.
2. Pull settlement reports — fees, refunds, reserves, payouts.
3. Match — use references for order-related fees and refunds; handle period-based costs separately.
4. Post — revenue by tax rate and country, expenses by fee type.
5. Reconcile — is the remaining balance explained by pending payouts, reserves or other documented movements?
6. Hand over — as a posting batch to DATEV or whichever system the firm uses.

Step 3 is where manual methods break down. A fee sits in a different report from the order it relates to, and the match runs on IDs, not on amounts.

At higher volumes not every order needs its own journal entry — comparable sales can be consolidated into summary entries as long as the underlying transactions stay traceable.

Where the margin actually goes

Review the additional cost categories separately from referral fees:

Fee type	When it is charged	What makes it awkward to book
Referral fee	per sale	straightforward, directly attributable
FBA fulfilment fee	per sale	depends on dimensions and weight, varies per item
Storage fee	monthly	relates to no single order, must be spread across periods
Aged inventory surcharges	according to the current Amazon statement	hits old stock, usually unnoticed until it appears
Advertising (PPC)	ongoing	lives in its own reports, not in the settlement report
Return processing fee	per return	arrives well after the original order

For a quick per-item calculation the Amazon fee calculator is enough; the full treatment of margin maths is in the post on Amazon fees.

VAT: review more than the destination country

Relevant inputs include dispatch and destination country, time of supply, customer type and the role of the marketplace. A bank statement does not provide all of them.

OSS can be used for transactions within the EU scheme; not every Amazon sale automatically qualifies. The German tax authority explains the OSS EU scheme. Review inventory movements and sales with your accountant. Our OSS/IOSS overview helps you prepare.

Stock transfers: the part the payout does not show

When stock moves between warehouses in different countries, payout data alone is insufficient for review. Include the available inventory reports and discuss possible local obligations with your tax adviser. OSS participation does not settle these questions by itself. Keep inventory movements distinct from sales.

When Shopify, eBay and TikTok Shop join

As soon as a second channel arrives, the work does not double — the number of formats does. Every marketplace names the same events differently, settles on its own cycle and delivers reports in its own structure.

Agree on consistent posting rules with your accountant. The marketplace alone determines neither the tax rate nor the account. Keep the channel, supply details and document reference visible so that different transactions are not combined without review.

If you also sell to Amazon rather than through the marketplace, a different logic applies: credit notes, co-op fees and allowances run through purchase orders and remittance advices rather than settlement reports. That is covered in the post on Amazon Vendor Central.

What has to reach the accountant

Agree on the files, documents and any access rights your accountant needs. Review accounts, tax keys, references and reconciled amounts using a test export. An automatically generated download does not replace that review.

What makes a DATEV import fail in practice — required fields, document links, open items, format errors — is covered in the post on DATEV export.

What of this can be automated

KudTax supports importing and preparing Amazon data. The Amazon integration offers API and file import. Check which reports and fields cover your workflow and which supporting documents are still needed. The DATEV export page explains the file handover.

Test a complete settlement period with FBA and/or FBM transactions, refunds and fees. Have your accounting team review the prepared handover. Register or request an Amazon demo to discuss suitability for your seller account. Current scope and costs are shown in pricing.

Frequently asked questions

Why does my Amazon payout not match my revenue?

A payout combines several movements. Fees, refunds, reserves and other adjustments may affect the amount. Explain the difference from the settlement report and account for separately paid costs outside that payout reconciliation.

Does every single order have to be booked?

Consolidation may be appropriate for eligible transactions. Agree on the requirements with your accountant and retain the connection to individual records. The linked summary-entry guide explains the workflow.

Do I need a foreign VAT registration if I use OSS?

Possibly. OSS covers distance sales to end customers, not the movement of your own goods into a warehouse abroad. If you use Pan-EU or CEE, check the inventory movement reports and settle the question with your tax adviser.

How does the data reach my accountant?

Use the agreed handover, such as a DATEV batch and its supporting documents. Accounts, tax keys, references and document handling need to match your accounting process.

Is a bank statement enough as a supporting document?

A bank statement records cash movements. Additional statements and documents explain the underlying sales, fees and refunds. Agree on complete documentation and retention with your accountant.