Ecommerce bookkeeping for Shopify and Amazon sellers comes down to one idea: a payout is not revenue. Every payout is sales minus fees, refunds and holds. Here is a 5 step way to record each piece and tie it to the bank.
Last updated November 2, 2026. Reviewed by Aryan Patel, founder of Senvora Group, a bookkeeping firm that supports CPA firms and business owners in the US and Canada. Our team reconciles Shopify and Amazon payouts in the order below. Everything about platform behavior below comes from the Shopify payout reconciliation report page, the Shopify payout details page, the Amazon settlement report documentation, the Sell on Amazon page on how seller payments work, and Intuit and IRS pages. Where a page does not say something, I tell you to check it.
Key takeaways
- A payout is the net amount deposited. It is not your sales number, so do not book it as revenue.
- Record gross sales, fees, refunds and holds as separate lines. Then match the payout total to the bank deposit.
- Shopify says held funds are not revenue from new sales. Amazon says reserved funds become the beginning balance of your next settlement period.
- The IRS page says the Form 1099-K threshold is more than $20,000 and more than 200 transactions. You report sales income either way, so keep your own records.
- Sales tax is set at the state level. Check your state revenue department for the rules that apply to you.
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Why a payout is not revenue
Open your bank feed and you will see a deposit from Shopify or Amazon. It is tempting to book that deposit as income. Do not.
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That deposit is what is left after the platform takes its cut. Fees come out. Refunds come out. Sometimes a hold comes out. What lands in your bank is a smaller number than what your customers paid.
If you book only the deposit, your sales look too low. Your expenses look too low too, because fees never show up. Your profit might look about right, but your margins and your sales tax picture will be wrong.
Here is the simple math. Payout equals sales minus fees minus refunds minus any reserve. Your job is to record each piece on its own line, then prove the total matches the bank.
A payout, line by line
This is a made up example to show the mechanism. The numbers are not from any real store and your own platform reports will look different.
| Line | Example amount | How to record it |
|---|---|---|
| Gross sales | 1,000 dollars | Sales or income account, not net of anything |
| Processing and selling fees | Minus 32.50 dollars | Expense account for platform and payment fees |
| Refunds | Minus 45.00 dollars | Reduce sales through a refund or contra income line |
| Reserve or hold | Minus 50.00 dollars | Not an expense and not a sale. Track it as money held by the platform |
| Payout to the bank | 872.50 dollars | The bank deposit. Match it, do not book it as income |
Check the math: 1,000 minus 32.50 minus 45.00 minus 50.00 is 872.50. If your deposit equals that, you are done. If it does not, something is missing.
What Shopify shows you
The Shopify payout reconciliation report page says the report covers transactions, fees, refunds, chargebacks, adjustments and payouts for a date range, so you can reconcile them with bank deposits. Activity is grouped by type. Groups that can appear include Charges, Refunds, Disputes, Adjustments, Fees, Reserves & Holds and Payouts.
A few details from that page are worth knowing:
- Held funds sit in a separate Reserves & Holds group. The page says they are not revenue from new sales.
- Payouts follow their own schedule. The page says totals for a date range might not match deposits for the same period.
- The report has a 3 day data delay, so recent transactions might not show yet.
- The report excludes Shopify billing fees and third party payment processors. Those need their own handling.
- The page says the report is not an accounting revenue statement. Finance reports are based on orders and sales and can differ in timing and totals.
For one deposit, the Shopify payout details page says to export that payout’s transactions. The CSV has a Fee column and a Net column. It also says a Deposited status means Shopify sent the payout to your bank. It does not mean the funds already posted. The page says banks typically take 1 to 3 business days.
Why is a payout lower than expected? The Shopify page on lower or missing payouts lists refunds, chargebacks, reserves, processing fees and adjustments, plus currency conversion fees, negative balance offsets and partial payout holds.
What Amazon shows you
The Sell on Amazon page on how seller payments work says Amazon generally settles seller accounts every two weeks and sends one disbursement to the bank on file. It adds that funds can take up to five business days to reach the bank after Amazon starts the payment.
It also describes the math in plain words. Amazon starts with the beginning balance, adds sales, subtracts expenses, adjusts for refunds, and pays out after withholding a reserve. The reserved amount becomes the beginning balance for your next settlement period. For deliveries, the page says Amazon typically reserves funds for seven days.
For detail, the Amazon settlement report documentation lists the Flat File V2 Settlement Report. It is tab delimited. Its fields include settlement-id, settlement-start-date, settlement-end-date, deposit-date, total-amount, transaction-type, order-id, amount-type, amount-description and amount. The page says all amounts appear in a single amount column, and the amount-type and amount-description columns hold the type of charge or fee.
That page does not state how long a settlement period is, and it does not say which refunds or reserves appear in each report. Check your own account for that. Do not assume.
A 5 step reconciliation routine
Run this for every payout. Monthly is the minimum. Weekly is better when volume is high.
- Pull the payout detail. For Shopify, export the payout’s transactions. For Amazon, use the settlement report for that deposit.
- Record gross sales. Sales go in at the full customer amount. Not net of fees.
- Record fees and refunds on their own lines. Fees go to expense. Refunds reduce sales.
- Park holds separately. A reserve is money the platform still owes you. Track it so it does not vanish from your books.
- Match the payout to the bank deposit. The payout total in your books should equal the deposit. If it does not, find the gap before you move on.
Watch for timing gaps. A sale in late October can land in a payout in early November. That is normal. A reconciliation that ignores it will look broken when it is not.
Can QuickBooks Online do this for you?
Partly. The Intuit guide to connecting Shopify to QuickBooks Online describes the Shopify Connector by QuickBooks. It syncs payments received, refunds and payouts. Confirming a payment creates a Sales Receipt, and fees create an Expense. Both sit in Undeposited Funds or Payments to deposit. Confirming the payout creates a Deposit for the net amount. Then in Bank transactions you select Match.
The Intuit guide to connecting Amazon Seller Central to QuickBooks Online describes the same flow for the Amazon Marketplace Connector by Intuit. It imports sales, refunds and payouts, and you can pull up to 12 months of history. It says Amazon pays out roughly every 14 days after deducting fees and adjustments. Both articles warn against adding the deposit manually in the bank feed.
One more thing from the Amazon article. It does not describe a manual file upload option. If you need to bring in a settlement file by hand, check Intuit’s current help pages for what is supported.
A connector helps, but it does not review itself. Someone still has to confirm each transaction, map adjustments to accounts and chase any deposit that does not match.
Form 1099-K and your sales numbers
The IRS page on understanding your Form 1099-K says payment apps and online marketplaces report when payments exceed $20,000 in more than 200 transactions. The IRS Form 1099-K threshold FAQs says the One, Big, Beautiful Bill reinstated that earlier threshold. Neither page names the tax years, so check the IRS site for the year you are filing.
The first IRS page also says income from selling goods or services must be reported no matter the amount of reported payments. It does not say whether the 1099-K figure includes fees or refunds, so do not assume it equals your net sales. Compare it to your own books and ask your CPA how to treat any difference.
This is one more reason to keep gross sales, fees and refunds apart. If you also pay contractors, our 1099 filing deadline guide covers that side. Senvora does bookkeeping. We do not prepare or file tax returns, so your CPA handles that part.
Sales tax
Sales tax is set by each state, so the rules depend on where you sell. The Intuit Shopify article says marketplace taxes go to Sales Tax Payable by default and that taxes you are responsible for are recorded on the sales receipt. Check your state revenue department for what you owe and when.
Where the books usually break
Watch for the usual slips. Payouts booked as income. Fees never recorded. Refunds netted against the wrong month. Holds that disappear. Our 5 QuickBooks setup errors we see most covers the setup errors we found in QuickBooks Online files, and the habits above help you avoid the ones that apply to stores.
If your books are months behind, start with our retroactive bookkeeping guide. Then keep each month clean with a quarter end close checklist.
Frequently asked questions
Is a Shopify or Amazon payout my revenue?
No. A payout is the net deposit after fees, refunds and any holds. Record gross sales, fees and refunds separately, then match the payout total to the bank deposit.
Why does my bank deposit not match my sales report?
Usually timing, fees, refunds or holds. The Shopify payout reconciliation report page says payouts follow their own schedule, so a date range may not match deposits for the same period. Compare your books to the payout detail, not to a sales total.
Are reserves and holds revenue?
Shopify says held funds are not revenue from new sales. Amazon says the reserved amount becomes the beginning balance for your next settlement period. Track them separately so they do not disappear from your books.
What is the Form 1099-K threshold?
The IRS page says reporting applies when payments exceed $20,000 in more than 200 transactions. Check the IRS site for the year you are filing, and report your sales income whether or not you receive the form.
Can QuickBooks Online connect to Shopify and Amazon?
Yes. Intuit has a Shopify Connector and an Amazon Marketplace Connector. Both create a Deposit from the payout so you can match it to the bank feed. You still need to review transactions and check that the match is correct.
Selling online as a solo owner? Start with clean accounts: how to separate personal and business finances as a freelancer.
Sources
- IRS page on understanding your Form 1099-K (irs.gov)
- IRS Form 1099-K threshold FAQs (irs.gov)
- Shopify payout reconciliation report page (help.shopify.com)
- Shopify payout details page (help.shopify.com)
- Shopify page on lower or missing payouts (help.shopify.com)
- Amazon settlement report documentation (developer-docs.amazon.com)
- Sell on Amazon page on how seller payments work (sell.amazon.com)
- Intuit guide to connecting Shopify to QuickBooks Online (quickbooks.intuit.com)
- Intuit guide to connecting Amazon Seller Central to QuickBooks Online (quickbooks.intuit.com)
Want help keeping your store books clean?
Senvora Group handles monthly outsourced bookkeeping for business owners and CPA firms, including platform payout reconciliations. You can also see our outsourced bookkeeping pricing breakdown, or DM Aryan. Which part of your payouts is hardest to tie to the bank right now?
