Key Principle

Your books should reflect:

• Gross payment received – the full amount your customer paid
• Payment processor fee – recorded as an expense, reducing net income
• Net deposit in your bank – matches the actual money that hits your account

Step 1: Identify the Transactions

Example from bank feed:

Step 2: Record Gross Payment

1. Go to + New > Receive Payment (or record invoice payment if linked).
2. Select the customer and invoice.
3. Deposit to: Undeposited Funds (or a clearing account if using Stripe/PayPal).
4. Enter the payment amount: $100 (gross amount).
5. Save.

Step 3: Record the Fee as an Expense

You have two options depending on how the bank shows the fee:

Option A: Fee Appears as a Separate Bank Feed Transaction

1. Go to Banking > For Review.
2. Select the fee transaction.
3. Category: Expense > Merchant/Processing Fees (create this account if needed).
4. Add a description: “Stripe fee for Invoice #123”.
5. Save.

Option B: Using a Clearing Account (Recommended for Net Deposits)

When you deposit the payment from Undeposited Funds to Checking:

• Bank Deposit → Received From: Customer A | Payment Method: Check | Amount: $100
• Subtotal: $100 → Deposit to Checking
• Less: Stripe Fees (Expense) | Amount: $3
• Net deposit: $97 → matches bank feed

This ensures the invoice is fully paid, fees are recorded as an expense, and the bank deposit matches QBO exactly.

Important Notes

• Do not record net deposit as income directly, this understates revenue.
• Always separate gross payment and fees to keep your P&L accurate.
• If multiple customer payments are included in a single net deposit, use Undeposited Funds or a clearing account to group them and record fees separately.
• For recurring Stripe/PayPal payouts, consider a clearing account integration or apps like A2X or Synder to automate this.

Summary