1. Deposits Are Net of Fees

Payment processors like PayPal and Stripe deposit net amounts into your bank account: Gross sale minus fees and refunds. QBO tries to match the bank feed deposit to the invoice amount, but the deposit is smaller than the invoice, so it won’t match automatically.

Example:

• Invoice = $100
• Stripe Fee = $3
• Bank deposit = $97 → QBO sees this as a different amount → no automatic match

2. Timing Differences

• Payments may be recorded in QBO as soon as they occur, via integration or manual entry.
• Bank feed deposits may appear days later, causing date differences.
• QBO auto-match is strict on amount and date, so it will not suggest a match if dates differ significantly.

3. Payments Went to Undeposited Funds

If payments are recorded to Undeposited Funds, the bank deposit won’t match the invoice until you deposit the payment from Undeposited Funds into the correct bank account.

4. Multiple Transactions in One Deposit

If one bank deposit contains multiple invoices (common with batch PayPal or Stripe payouts), QBO cannot automatically match it, auto-match only works one-to-one.

5. Different Customer Names or Invoice Numbers

Auto-match relies on exact invoice numbers and customer names. Small differences (e.g., “John Smith” vs. “John A. Smith”) can prevent a match.

Option 1: Use Undeposited Funds or a Clearing Account

1. Record the payment against the invoice → deposit to Undeposited Funds.
2. When the net deposit hits your bank, record a Bank Deposit from Undeposited Funds.
3. Match the net deposit in the bank feed to this deposit, this avoids discrepancies caused by fees.

Option 2: Record Fees Separately

• Create an Expense account called “Stripe/PayPal Fees.”
• Enter fees as an expense when depositing net amounts.
• The invoice stays fully paid, and your bank deposit matches the net received.

Option 3: Use a Third-Party Integration

Apps like A2X, Synder, or Webgility can:

• Import gross sales and fees separately.
• Apply payments to invoices correctly.
• Create deposits that match the bank feed automatically.
• Handle multi-invoice payouts without manual adjustments.

Option 4: Manual Match

1. Go to Banking → Reviewed Transactions.
2. Select the deposit.
3. Click Find Match → select the related payment or invoice(s).
4. Enter the net amount and optionally record fees as an expense.

This ensures the invoice is marked paid and your bank feed reconciles correctly.

Key Takeaways