How do I get clean accounts from Shopify, Amazon and wholesale sales?

Why the numbers never match the bank

A deposit from Amazon or Shopify is not your sales figure. It is sales, minus fees, minus refunds, minus any money held back, plus or minus adjustments. Say, with made-up numbers, a customer pays $100, but $88 lands in your bank. If you book $88 as income, your sales look too low and your fees disappear. If you book $100 and never record the fee, your books never balance.

The fix is to record the gross sale, the fees and the refunds as separate lines, and then let the bank deposit clear against them. That is the whole idea of ecommerce accounting. The rest is detail.

The clearing account, explained

A clearing account is a temporary account, one per channel. Sales, fees and refunds post into it. When the payout hits your bank, the deposit comes out of it. At the end of the month the balance should be near zero, apart from sales that have not paid out yet. If it is not zero, something is missing.

Here is a made-up example for one Shopify payout:

Line	Amount
Gross sales	$1,000.00
Refunds	-$60.00
Processing fees	-$31.00
Net payout to bank	$909.00

In your books, income gets $1,000, refunds get $60, fees get $31, and the clearing account takes the difference. Then the $909 deposit clears it to zero. Each channel gets its own clearing account, so you can see which one is out of balance.

Where each channel keeps the data

Shopify

Shopify is an online store platform. With Shopify Payments, its own payment service, funds go to your bank account or a Shopify Balance account after each order. Shopify's help pages describe a payout details export and an activity report that shows how your balance changed, including fees, so you can reconcile payouts. Payouts can be daily, weekly or monthly, and they can be held in reserve or come in lower than expected, so check why before you assume an error. Orders paid through PayPal or other gateways pay out somewhere else, and need their own clearing accounts.

Amazon

Amazon pays you by settlement. Amazon's seller API documentation says settlement reports cannot be requested or scheduled, because Amazon creates them automatically. The current Flat File V2 report, which replaced the older flat file and XML versions, lists each charge in three columns: amount-type, amount-description and amount. That layout helps, because new fee types appear as new rows and do not break the format. Amazon fees include referral fees, fulfillment fees, storage and ads. Check whether a settlement period crosses a month end in your own reports, because that is a common cause of mismatches.

Wholesale

Wholesale works differently. You send an invoice, and the buyer pays days or weeks later by bank transfer or card. That is accounts receivable, not a payout. Post the invoice when you send it, and match the payment when it arrives. Do not mix it with channel clearing accounts.

Tools that do the posting for you

These tools read payouts and post a summary into your accounting software. QuickBooks Online and Xero are both subscription accounting packages for small businesses. For a view on whether to stay on QuickBooks, see my QuickBooks alternatives guide.

• A2X. Turns payout data from Amazon, Shopify, eBay, Etsy (a marketplace for handmade and vintage goods), Walmart, TikTok Shop and PayPal into summaries for QuickBooks Online, Xero or NetSuite (Oracle's business software for larger companies). Pricing starts at $29 a month for most channels and $79 for Walmart, as of November 2026. It also has a multi-channel option. Check the A2X pricing page for your channel mix.
• Link My Books. Posts settlements for Amazon, eBay, Shopify, Etsy, Walmart and TikTok Shop into Xero or QuickBooks. Its site also lists WooCommerce (a shop plugin for WordPress) and Square (a card payment and point-of-sale service) as channels, with Xero as the accounting link. It lists cost-of-goods tracking, P&L by channel and payout reconciliation. A paid plan can go back up to 24 months of settlements, depending on the plan. Its price depends on orders and channels: in US dollars its calculator showed $35 a month for 500 orders on one sales channel and $77 for 3,000 orders across two, as of November 2026.

Both charge by channel or order volume, so your monthly cost rises as you grow. For a seller with three channels the cost is small next to the hours it saves, and next to the cost of a bookkeeper fixing it by hand. If you want a general view of AI in the books, read about AI bookkeeping.

How to set up Shopify and Amazon with QuickBooks, step by step

1. Create one clearing account per channel in your chart of accounts, such as "Shopify clearing" and "Amazon clearing".
2. Create income, refund and fee accounts. Split fees by type if you want to see them: processing, referral, fulfillment, advertising.
3. Pick a sync tool or decide to post by hand. Connect each channel to it.
4. Map each payout line to an account. Do this once, carefully.
5. Choose a start date and load stock cost from that date forward. Do not try to rebuild years of history first.
6. Post the first summaries, then check that each clearing account reaches zero when the bank deposit lands.
7. Reconcile the bank feed monthly and look at any clearing balance left over.

Do not forget cost of goods

Clean sales and fees still do not give you profit. You need cost of goods sold, which is what you paid for the stock you sold. Many sellers post purchases as expenses when they pay a supplier, which makes profit look terrible in a month you restock and great in a month you do not. Post stock purchases to an inventory asset account and move the cost to cost of goods as items sell. Your stock tool or your accounting sync should help with this. If you use a stock system such as an inventory management system, ask whether it can send the cost figures to your books.

The reports an owner needs each month

• Profit and loss by channel. Sales, refunds, fees and cost of goods for each.
• Clearing account balances. Anything not at or near zero needs a note.
• Fees as a percent of sales, by channel. A creeping number tells you when a channel stopped paying.
• Accounts receivable aging. Wholesale invoices that are late, grouped by how many days.
• Inventory value. It should agree with the stock on your shelves and at Amazon.

A simple template is one sheet with a row per channel and columns for gross sales, refunds, fees, cost of goods and margin. Fill it from your books every month. If you want the Amazon part in more depth, see my guide to the Amazon seller profit and loss statement.

What the books will not show

Accounting is a record of the past, grouped into months. It is poor at answering "which product made money on which channel". It also will not show ad spend per product or the true cost of a return. For that you need a profit report on top, which I cover in the ecommerce profit dashboard guide. Also remember that the sales tax and VAT rules vary by place, so ask your accountant. I am not giving tax advice here.

Common failure points

• Booking the bank deposit as income.
• One clearing account for all channels, so you cannot find the gap.
• Payouts that straddle a month end, left unsplit.
• Refunds posted in a later month than the sale, with no note.
• Fees taken from the payout, such as ads or storage, that were never coded.
• Wholesale deposits mixed into channel clearing accounts.

How I'd approach this

I would not post by hand past about 100 orders a month. Pick a sync tool, set up clearing accounts first, and start at the beginning of a month so your cut-off is clean. Ask your accountant to sign off the account setup once, since it is the part that is hard to fix later.

After that, add one owner report that is separate from the books: profit by product and channel, built from the same data. If you have outgrown ready-made tools because you have unusual rules, such as shared stock costs or wholesale price tiers, a small custom report that reads your payout data and your costs can be built to fit. That is the kind of job I take on.