Where to find your Shopify fees
Your Shopify fees are not in any sales report, because Shopify's net sales formula (gross sales minus discounts minus sales reversals) never takes fees out. They sit in three other places, depending on who charged them: card fees in Finance > Payouts, Shopify's transaction fees on your Shopify bill, and a third-party processor's fees in that processor's own statements.
Why sales reports never show fees
A sales report is built from orders. A fee is a cost of collecting the money for those orders, and Shopify records it on the payments side instead; its own payments report says it "isn't a statement of revenue for accounting purposes". So "sales minus fees" is always two sources put side by side, and when you build it yourself you have to choose which dates to use. Why that also makes a payout smaller than sales is a related question; the net sales formula itself is on gross vs net sales.
The four kinds of fee, and where each one lives
1. Shopify Payments processing fees (card fees)
- Per transaction: Finance > Payouts > View transactions > Export, choose "Items by date" and a CSV file, then export the items. Each row has an Amount, a Fee and a Net. Add up the Fee column for the month.
- Per period: the Shopify Payments activity report, under Finance > Documents (Money > Payments volume on stores with a Money page), shows the total fees deducted from your balance in the date range you pick. Its refunds total includes related fee adjustments, and its disputes total includes dispute fees.
- In Analytics: a metric called Payment processing fees reports the fees you pay per order through Shopify Payments. In ShopifyQL, each row of the fees data ties to an order and the date of the sale.
2. Shopify transaction fees
With Shopify Payments you don't pay a transaction fee. Stores that use a third-party provider instead pay Shopify a transaction fee on top of the provider's own charges. These are not in the payments report, which "doesn't include Shopify billing fees"; they are on your Shopify bill, as transaction fee charges. Go to Settings > Billing, open a bill under Past bills, and export it.
3. Third-party processor fees
PayPal, buy-now-pay-later providers and other gateways keep their own fees. The Shopify Payments activity report leaves out third-party payment processors, so those fees are in each provider's statements, not in Shopify. Orders paid that way are also missing from your payout list, see why order counts differ.
4. International fees
If you sell across borders, Analytics reports currency conversion and Managed Markets fees as their own figures. Your subscription and app charges are on the Shopify bill too; those are store running costs, not per-order fees.
Sources: Shopify Help Center: Viewing and exporting payout details · Shopify Help Center: Shopify Payments activity report (read 29 Oct 2026) · Shopify Help Center: Viewing your payout fees · Shopify Help Center: Managing your Shopify bills · Shopify Help Center: Types of charges on your bill · Shopify Help Center: Analytics data points (fields) reference · Shopify developer docs: ShopifyQL fees data
Why three fee totals for the same month can disagree
The surfaces use different dates. The ShopifyQL fee data dates each fee to the sale. The payout export's Transaction Date column is when the transaction occurred. The activity report shows balance activity within your range. Our reasoning from those definitions: a card captured on 1 November for an order placed on 31 October falls in October on the first surface and in November on the other two, and a refund or dispute fee lands in the month it happened, not the month of the original sale. None of these totals is wrong. Pick one basis and write it next to the number.
How to total one month of fees
- Choose your basis. For margin, date fees to the sale. For bookkeeping, use when the money moved.
- Shopify Payments: export Items by date for the month and add up Fee. Use the Type column to keep charges, refunds and disputes apart.
- Shopify bill: export each bill that covers the month and take the transaction fee lines.
- Each other processor: take that month's fee total from its statement.
- Add them up, and write down the basis and the four sources.
A worked example (HYPOTHETICAL)
| Net sales, Shopify Analytics | $20,000.00 |
| Shopify Payments, Fee column, charges dated October | $612.40 |
| Shopify Payments, one dispute fee | $15.00 |
| PayPal fees, from the PayPal statement | $96.30 |
| Total fees | $723.70 |
Invented numbers for one October, not a real store. The fees come to $723.70 on $20,000.00 of net sales, about 3.6 cents of every sales dollar. In the same hypothetical store, Analytics' Payment processing fees for October could show a different Shopify Payments figure from $612.40, because it dates each fee to the sale while the export dates it to the transaction. Neither total is an error.
What ProfitRoot does with this
ProfitRoot ties Net Sales to Shopify to the cent first. Payment fees are a separate layer: add the Shopify Payments payouts file (the export with a Fee column) on Connections and the fees move into contribution margin. The other payments export, the one with no Fee column, is refused with the reason named. Until a payments file is added, that layer says which file it needs and shows no number, and fees from other processors are named as not covered rather than counted as zero. Free to install; Pro $49 a month; Firm $149 a month; every feature free during the founding period.
Common questions
Where can I see all my Shopify Payments fees for a month or a year?
Go to Finance > Payouts > View transactions > Export, choose Items by date and a CSV file, export the items and add up the Fee column. For a period total, the Shopify Payments activity report under Finance > Documents (Money > Payments volume on stores with a Money page) shows the fees deducted from your balance in the range you pick.
Why can't I see monthly sales minus fees in one Shopify report?
Sales reports are built from orders. Shopify defines net sales as gross sales minus discounts minus sales reversals, and processing fees are recorded on the payments side. To get sales minus fees you combine two sources and say which dates you used.
Are Shopify transaction fees the same as processing fees?
No. Processing fees are card fees taken from your Shopify Payments balance. Shopify says that with Shopify Payments you do not pay a transaction fee. Stores that use a third-party provider instead pay Shopify a transaction fee, and it appears on the Shopify bill.
Why doesn't the Shopify Payments activity report include my PayPal fees?
Shopify says the report does not include third-party payment processors or Shopify billing fees. PayPal fees are in your PayPal statements. Shopify transaction fees are on your Shopify bill.
Are Shopify fees part of cost of goods sold?
Not in Shopify's reports. Shopify calculates gross profit as net sales minus cost of goods sold, and payment fees are not part of that formula. Where fees sit in your books is your accountant's call. In a margin breakdown they usually come below gross profit, in contribution margin.
What this does not tell you
Where each fee belongs in your books, and what can be deducted for tax, are questions for your accountant; for how fees show up once a ledger sync is running, see QuickBooks and Shopify after a sync. Card rates differ by plan and country; check yours under Settings > Payments > Shopify Payments > Manage.
The section on dates is our reasoning from Shopify's definitions, not a Shopify statement. The worked example is hypothetical.
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Sources last checked 2026-10-30.