Thank you for contacting us about the fee when processing an invoice in QuickBooks Online, linhmai2512.
Usually, fees when processing payments are taken from the employer side. And, if you're using an instant deposit, there's an additional 1% fee of the total amount for this process.
Check out this link for additional information: Get instant deposits in QuickBooks Online.
For further discussion, I recommend contacting our QuickBooks Merchant Service Team. They can check those charges and fees on your account. Please visit this page to select your subscription and chat with a representative: Contact Payments.
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