Why QuickBooks Online Shows “Net of Fees”

When Shopify (or a connected app like Shopify Payments, A2X, or Synder) sends transactions to QBO, it often records only the amount that actually hit your bank account i.e.,

Net = Gross Sales – Shopify Fees – Refunds – Taxes – Discounts

So instead of showing $1,000 in sales and $30 in fees, QBO may just show a $970 deposit, because that’s what your bank received. This is accurate from a cash perspective but hides:

• Gross revenue
• Merchant processing fees (deductible expenses)
• Sales tax collected (which you must remit)

The Right Way: Record Gross Sales and Fees Separately

You have two main options depending on how much detail you want.

Option 1: Use a Clearing / Shopify Payout Account (Best Practice)

This method matches how most accountants track e-commerce platforms.

1. Create a Clearing Account
   • Go to → Chart of Accounts → New
   • Type: Bank
   • Name: “Shopify Clearing” or “Shopify Payments Clearing Account”
2. Record Gross Sales
   • Use a Sales Receipt or Journal Entry to record the day’s total:
   • Sales Income: Gross sales amount
   • Sales Tax Payable: Taxes collected
   • Shopify Fees Expense: Merchant fee as a negative line item
   • Deposit to: Shopify Clearing Account
3. Record Shopify’s Bank Deposit
   • When Shopify deposits $970 into your real bank, record a Transfer:
   • From: Shopify Clearing
   • To: Checking Account
   • Amount: $970
   • The clearing account should now net to $0 once fees and deposits balance.

Result:

• Gross sales: $1,000
• Shopify fees: $30 expense
• Bank deposit: $970
• All accounts reconcile perfectly

Option 2: Use an Integration That Posts Gross Amounts Automatically

If you don’t want to post entries manually, use a Shopify–QuickBooks connector that separates sales and fees properly.

• A2X for Shopify: creates detailed, accrual-basis entries for sales, refunds, fees, and taxes.
• Synder: posts daily summarized journal entries with gross income and fees.
• QuickBooks Commerce / Intuit Shopify connector: configurable to record gross or net.

Tip: Always choose “Record sales gross and fees separately” during setup if the option appears.

Option 3: Manual Journal Entry (If Few Transactions)

For a few months of adjustment:

This converts the net deposit into a true gross sale.

Common Mistakes

• Recording the net deposit as Sales Income → hides fees and overstates profit.
• Double-recording sales (one from Shopify, one from QBO).
• Not using a clearing account → reconciliation problems when multiple payouts overlap.
• Forgetting to separate sales tax from income.

Best Practice Summary