Ecommerce accounting

    Accounting for Amazon FBA and FBM sellers

    Amazon pays you a net deposit after fees, refunds and adjustments. Good books start by breaking each settlement back out. Here's how we handle settlements, inventory, sales tax and income tax for Amazon sellers.

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    • Last reviewed October 7, 2026
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    How should an Amazon seller handle accounting and taxes?

    Your Virtual CPA, a licensed CPA firm, does accounting for Amazon FBA and FBM sellers. We reconcile each settlement report to your bank deposits, record Amazon fees and refunds, track inventory and cost of goods sold, review sales tax exposure, and prepare business tax returns with your 1099-K in mind. Book a free 30-minute call to review your setup.

    Best for

    Best for Amazon sellers using FBA, FBM or both, often alongside a Shopify store or other channels, who want CPA-reviewed books and business tax returns from one firm.

    Settlement reports, fees and inventory

    • Settlement reconciliation. Each settlement includes orders, refunds, fees and adjustments behind one disbursement. We record sales, refunds and each fee type at the gross level and tie the net amount to your bank deposit.
    • Fees. Referral fees, fulfillment fees, storage fees, advertising and subscription charges are recorded in separate accounts, so you can see what each one costs you.
    • Reimbursements and adjustments. Lost or damaged inventory reimbursements and other adjustments are recorded so they don’t distort sales or cost of goods sold.
    • Inventory and cost of goods sold. We track inventory as an asset and record cost of goods sold as units sell, using a method that stays consistent and matches your tax return.

    Sales tax and income tax

    Sales tax. In states with marketplace facilitator laws, Amazon calculates, collects and remits state sales tax on orders it facilitates for third-party sellers. Amazon notes that some local taxes are not included. That covers your Amazon orders only. Sales on your own website or Shopify store are your responsibility, and registration rules vary by state.

    Form 1099-K. Third party settlement organizations must file Form 1099-K when a payee’s gross payments exceed $20,000 and there are more than 200 transactions. Payment card transactions have no threshold. The 1099-K shows gross payments, not profit, so your books need to explain the difference.

    Income tax. We prepare the business return, whether you file as a sole proprietor, partnership, S corporation or C corporation, and plan estimated taxes during the year. See business tax preparation.

    How it works with us

    1. Free 30-minute call about your channels, fulfillment model, inventory and where the books stand.
    2. Access. You add us to QuickBooks or Xero and give report access in Seller Central, any other sales channels and your bank feeds.
    3. Review and cleanup. We review prior months and quote any cleanup separately.
    4. Monthly close. We reconcile every settlement and account and send monthly financial statements.
    5. Tax. We review sales tax registrations and prepare your business income tax returns.

    Fees are transparent, fair and quoted upfront, in writing. Switching from another bookkeeper? See switching your Shopify or Amazon bookkeeper.

    Amazon seller accounting at a glance

    AreaWhat we do
    SettlementsRecord gross sales, refunds and fees; tie net to bank deposit
    FeesSeparate accounts for each Amazon fee type and advertising
    InventoryTrack inventory as an asset; record cost of goods sold as units sell
    Sales taxAmazon collects in marketplace facilitator states; we review your other channels
    1099-KFiled when gross payments exceed $20,000 and transactions exceed 200; we reconcile it to your books
    Income taxBusiness returns and estimated tax planning

    Expert CPAs. Personal attention.

    Selling on Amazon? On a free 30-minute call we'll look at your settlements, inventory and sales tax setup and tell you what we'd change.

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    Frequently asked questions

    In states with marketplace facilitator laws, Amazon calculates, collects and remits state sales tax on the orders it facilitates for third-party sellers. Some local taxes are not covered. Sales you make outside Amazon, such as on your own website or Shopify store, are not covered by Amazon’s collection.

    It depends on the state and on your other sales. In Virginia, for example, a seller whose sales all go through a marketplace facilitator generally does not need to register to collect Virginia sales tax. Other states have their own rules, and sales through your own store can create a registration requirement.

    Third party settlement organizations must file Form 1099-K when a payee’s gross payments for goods or services exceed $20,000 and there are more than 200 transactions. Payments processed as payment card transactions have no threshold. Either way, you must report all business income on your tax return.

    Amazon pays you one net amount per settlement period, after fees, refunds, reimbursements and other adjustments. Recording only the deposit understates both sales and expenses. The fix is to record each settlement at the gross level and tie the net total to the bank deposit.

    Track inventory as an asset when you buy it, including inbound shipping where appropriate, and record cost of goods sold as units sell. The method should be consistent month to month and match how inventory is reported on your tax return. A CPA can help you pick a method that fits your size.

    Yes. You add us to QuickBooks or Xero and give report access in Seller Central. We review the books and the last close, then start from a month you choose, with cleanup first if any months need it.