Amazon doesn't deposit your revenue. It deposits the leftovers after fees, refunds, FBA storage, advertising, and a dozen other line items. Reconciling that deposit to QuickBooks Online means matching every line item to the right account, not just the gross sales number.
Done manually, a single Amazon settlement reconciliation takes a bookkeeper about 90 minutes. Done with the wrong assumptions, the books look fine in QuickBooks but are wrong by thousands of dollars in ways that don't surface until a tax filing.
In Seller Central, go to Reports → Payments → Statement View. Each settlement period (typically two weeks) generates one statement. Click Download flat file to pull the V2 settlement report as a CSV.
Amazon's settlement reports include transaction types like Order (sales), Order (sales tax), Order (shipping charged), Refund, FBA fee, FBA storage fee, Referral fee, Advertising (PPC), Service fee, Adjustment, and Reserve. Each posts to a different QuickBooks account.
The most common mistake at this step is lumping referral fees into sales (so revenue looks lower than it is) or treating reserves as a fee (so the books are off by the reserve balance each period). Reserves are timing. The money is yours, Amazon is just holding it temporarily.
The sum of every line in the settlement report equals the deposit amount that hit your bank account. In QuickBooks, find the matching bank deposit. Click Add Transaction Details and split the deposit across each of the accounts, using the amounts from your categorized settlement report.
If the math is off by even a few cents, something was miscategorized. Figure out which transaction type didn't add up and fix the categorization.
The settlement deposit is revenue and fees. It does not include cost of goods sold. To complete the period's books, you also need to post the inventory cost of the units that sold.
If you sell SKUs at different cost layers, you need to apply FIFO or weighted-average accounting to know which cost layer the shipped units came from. Doing FIFO by hand for 200 SKUs is a full day of work per period.
If you have nexus in marketplace-facilitator states, Amazon collects and remits sales tax for you. The settlement report shows the tax collected and the tax remitted by Amazon. These should net to zero in your sales tax liability account.
Refunds in Amazon settlements include the customer refund, the lost referral fee, and the unsellable inventory write-down for items that can't be re-listed. Each piece posts differently.
The six steps above describe what ConnectBooks automates. The settlement file is parsed, transaction types are mapped to the correct QuickBooks accounts, FIFO COGS is applied per SKU based on the inventory ledger, sales tax is reconciled by jurisdiction, and unsellable returns are categorized separately. The 90 minutes of manual work compresses to roughly two minutes of review.
Every settlement period. For US Amazon, that's every two weeks.
That happens when a settlement spans a month-end and Amazon delays the deposit. The settlement amount should still equal the deposit amount exactly, just delayed by a few days.
Both. The wholesale cost of the unit posts to COGS. The FBA fulfillment fee is conventionally tracked separately. Sub-accounts under COGS work well.
Skip the 90-minute reconciliation. See how ConnectBooks reconciles Amazon settlements to QuickBooks automatically, with FIFO COGS, unsellable returns, and marketplace-facilitator tax handled correctly. 30-day free trial.
Running an e-commerce business comes with plenty of challenges, but ConnectBooks is here to make your life easier. With real-time insights, seamless integrations, and detailed tracking of your profitability and inventory, you can stay ahead of the game. Whether you’re selling on Amazon, Shopify, Walmart, TikTok or eBay, ConnectBooks helps you manage your finances with 100% accuracy and confidence, so you can focus on growing your business.
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