Complete Guide to Amazon Seller Accounting: From Sales to Settlement

Whether you’re just starting as an Amazon seller or scaling your business fast, one thing becomes clear quickly: keeping your finances in order is just as important as making sales.

Selling on Amazon comes with unique accounting challenges—frequent pay-outs, multiple fees, and complicated reports. Without the right system, it’s easy to lose track of what you’re earning (and what Amazon is keeping).

In this guide, we’ll walk you through everything you need to know—from tracking sales and expenses to understanding settlement reports and when to bring in an expert.

Why Amazon Accounting Needs a Specialized Approach

Amazon isn’t like other ecommerce platforms. The platform handles a lot for sellers—fulfilment, storage, returns, and even sales tax in many cases—but it also comes with layers of hidden complexity in how your earnings are processed and reported.

Here’s why Amazon accounting stands out:

  • You get paid every 14 days, but those payouts include dozens (sometimes hundreds) of fees and deductions.
  • Refunds, returns, storage charges, and reimbursements can affect your true profits.
  • Without clear reports, it’s difficult to know which products are truly making you money.

That’s where clean and customized bookkeeping makes all the difference.

FBA vs. FBM Accounting: What’s the Difference?

Amazon sellers typically choose between two fulfilment models—FBA (Fulfilled by Amazon) and FBM (Fulfilled by Merchant). Each has its own accounting considerations:

Amazon FBA (Fulfilled by Amazon)

Amazon handles storage, shipping, and customer service. You just send your products to their warehouse.

Accounting tasks include:

  • Tracking inventory costs and shipping to Amazon
  • Recording FBA fees (which vary by size and weight)
  • Managing reimbursements for lost or damaged items
  • Monitoring long-term storage fees

Amazon FBM (Fulfilled by Merchant)

You store and ship products yourself (or via a 3rd-party warehouse).

Accounting tasks include:

  • Recording shipping and packaging costs
  • Tracking order returns and refunds
  • Managing your own inventory systems
  • Logging any Amazon seller fees

amazon accounting

What Should Amazon Seller Bookkeeping Include?

Accurate bookkeeping helps you understand your true profitability, stay compliant with taxes, and make smarter business decisions. Here’s what it should cover:

1. Recording Sales and Fees

Instead of recording each order manually, use Amazon’s settlement reports to summarize:

  • Total sales
  • Shipping income
  • Discounts and promotions
  • Amazon’s seller and referral fees

2. Tracking Inventory and Cost of Goods Sold (COGS)

You should always know:

  • How much inventory you have
  • How much it costs you to produce or buy it
  • How much profit you’re making on each product

Accurate COGS reporting is essential for measuring real performance.

3. Handling Returns and Refunds

Amazon may automatically issue refunds and even reimbursements. Your books need to reflect:

  • Money refunded to customers
  • Restocking fees
  • Products that are returned damaged

4. Reconciliation of Amazon Settlements

Every few weeks, Amazon deposits money into your bank account. But that’s not just sales—it includes:

  • Deductions for fees
  • Adjustments for returns
  • Advertising charges (if you’re running PPC)

You need to reconcile this data with your accounting software to ensure accuracy.

Do You Need Accounting Software for Amazon Sales?

Yes—especially if you’re selling at scale. Manual tracking in Excel won’t cut it for long. The good news is there are tools that integrate directly with Amazon.

Recommended Tools:

  • Xero + A2X – A reliable combo for automatically importing and categorizing settlement data.
  • QuickBooks Online + Link My Books – Great for managing FBA and FBM accounts side-by-side.
  • TaxJar or Avalara – To simplify sales tax compliance.

At Accountsly, we use tools like these to build a reliable accounting system tailored to Amazon businesses.

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What About Sales Tax and Income Tax?

Sales Tax

Amazon may collect and remit sales tax on your behalf in some U.S. states (under marketplace facilitator laws). But you may still need to:

  • File returns
  • Track where tax was collected
  • Register in certain states

Income Tax

You’re responsible for reporting all Amazon income and expenses for your year-end taxes. That means keeping clean records of:

  • Revenue
  • COGS
  • Operating expenses (software, freelancers, shipping, etc.)
  • Advertising spend

When Should You Hire an Amazon Accountant?

If you’re growing fast or selling across multiple marketplaces (Amazon US, UK, Canada, etc.), handling accounting on your own becomes time-consuming and risky.

You should consider hiring an Amazon specialist accountant if:

  • You’re confused by Amazon’s payout reports
  • You’re unsure about tax compliance
  • You want clear monthly financial reports
  • You’re preparing to apply for funding, a loan, or even planning an exit

At Accountsly, we provide full-service Amazon accounting—including bookkeeping, reporting, inventory tracking, and tax filing—for FBA and FBM sellers.

Work With Amazon Accounting Experts Who Understand Your Business

We’re not just generic accountants—we specialize in ecommerce and Amazon seller accounting. Whether you sell supplements, apparel, electronics, or handmade goods, we help you:

  • Keep accurate financial records
  • Understand your profitability
  • Plan ahead for taxes
  • Grow with confidence

Need Help with Your Amazon Seller Books?

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