What Are Shopify Fees and Where Do They Go in QuickBooks?
Shopify takes a cut of every sale. Here's what those fees are, how much they cost, and how PaydayBooks handles them in your books automatically.
If you've ever looked at a Shopify payout and thought "this is less than I expected," fees are almost always the reason. Here's a plain-English breakdown of what fees Shopify charges and how PaydayBooks makes sure your books reflect them correctly.
Payment processing fees
Every time a customer pays by credit or debit card, Shopify charges a payment processing fee. The exact rate depends on your plan:
- Basic Shopify: 2.9% + 30¢ per transaction
- Shopify: 2.6% + 30¢ per transaction
- Advanced Shopify: 2.4% + 30¢ per transaction
These fees are automatically deducted from your payouts. On a $100 sale, you might receive $97.10 after fees on the Basic plan. Over a month with thousands of transactions, this adds up to a real number.
Your Shopify subscription fee is separate
The monthly plan you pay to Shopify ($39, $105, or $399 per month) is billed separately to your credit card. It does not come out of your payouts. You'll want to record that separately in QuickBooks as a software subscription expense.
Dispute fees
If a customer files a chargeback and wins, Shopify charges a $15 dispute fee (in addition to refunding the transaction amount). This is deducted from your payout. If you win the dispute, you get the $15 back.
Where do fees appear in QuickBooks?
Here's the important part: because Shopify's processing fees are already deducted from your payout before it hits your bank, you don't see them as a separate line item on your bank statement. They're implied by the difference between your gross sales and the net deposit.
PaydayBooks handles this correctly. It records the gross SalesReceipt (before fees) and the exact net Deposit (after fees). The difference between those two numbers — your fees — is captured implicitly through the clearing account. Your income statement shows your full revenue, your bank reconciliation shows the actual deposit, and everything balances.
No manual fee tracking required. No adjusting entries. PaydayBooks calculates and records everything automatically every time a payout lands.