What QuickBooks Charges You for Processing Payments

QuickBooks Payment Processing Fees Explained

QuickBooks charges you a fee every time a customer pays you by card, bank transfer, or other electronic method. The fee comes out of the payment before the money lands in your account—so if a customer sends $100 and the fee is $2.99, you receive $97.01. The exact amount depends on which QuickBooks product you use, how the payment is made, and whether you process it online or in person.

QuickBooks does not charge a monthly subscription for payment processing itself. You pay only when money actually moves. This is different from some other payment processors, which charge a flat monthly fee whether you process payments or not. However, if you use QuickBooks Online Plus or other subscription tiers, you are already paying a monthly fee for the accounting software—payment processing is an add-on cost on top of that.

Key Takeaways

• QuickBooks charges a percentage of each payment plus a flat per-transaction fee, with rates varying by payment method and product tier.
• Card payments (Visa, Mastercard, Amex, Discover) cost more than bank transfers (ACH), which cost more than invoices paid through QuickBooks itself.
• In-person card payments (swiped or tapped) usually cost less than online or phone payments because the card is physically verified.
• You can see the exact fee before you process a payment, and QuickBooks shows it as a separate line item in your transaction history.
• Fees are deducted automatically from the payment; you do not receive an invoice or bill for them separately.

Card Payment Fees: Online, Phone, and In-Person

Card payments carry the highest fees because the card networks (Visa, Mastercard, American Express, Discover) take a cut, and QuickBooks takes a cut on top of that. The fee is usually stated as a percentage plus a flat amount per transaction. For example, you might see "2.9% + $0.30" for an online card payment. On a $100 payment, that would be $2.90 + $0.30 = $3.20 total.

In-person payments (card swiped or tapped at a reader) cost less than online or phone payments because the card is physically present and verified, which reduces fraud risk. Online and phone payments cost the same and carry a higher percentage because the card is not in hand. If you use QuickBooks Online and accept cards through the built-in payment button, the rates are set by QuickBooks and do not vary by card type (Visa costs the same as Amex).

If you use a separate card reader (like a Square reader or QuickBooks card reader) plugged into your phone or tablet, the fees may differ slightly. Check your QuickBooks settings or your reader's documentation to see which rate applies to your setup.

Bank Transfer and ACH Fees

Bank transfers (also called ACH payments) cost much less than card payments because no card network is involved. The fee is usually a flat amount per transaction—often $0.50 to $1.00—with no percentage. On a $100 bank transfer, you might pay $1.00 total, compared to $3.20 for a card.

The trade-off is speed. Bank transfers take 3 to 5 business days to clear, while card payments clear in 1 to 2 days. If you need the money fast, you pay more for a card. If you can wait, a bank transfer saves you money. Some customers also prefer bank transfers because they do not want to give you their card number.

QuickBooks shows the ACH fee before the customer pays, so they can see what they will be charged. The fee is deducted from the payment just like a card fee.

Invoice Payment Fees Through QuickBooks

If you send a customer an invoice through QuickBooks Online and they pay it by clicking a button in the email or on your invoice portal, QuickBooks charges a fee for that payment too. The fee structure is the same as card or bank transfer payments—it depends on which payment method the customer chooses when they pay the invoice.

Some customers will choose to pay by card (higher fee to you), and some will choose bank transfer (lower fee to you). You cannot control which method they pick, but you can see the fee before the payment is processed. If a customer is about to pay by card and you want to save the fee, you could ask them to use bank transfer instead—though this only works if they are willing to wait the extra few days.

How Fees Appear in Your QuickBooks Account

When a payment comes in, QuickBooks shows the fee as a separate transaction or as a deduction on the deposit. In QuickBooks Online, you will see the gross payment amount, the fee amount, and the net amount (what you actually receive) listed separately. The fee is usually categorized as "Payment Processing Fees" or "Merchant Fees" in your expense accounts.

You can run a report to see all your payment fees by date, payment method, or customer. This helps you understand which payment methods cost you the most and whether it makes sense to encourage customers to use cheaper methods. The fee is deducted automatically—you do not have to do anything or pay a separate bill.

If a payment is refunded, the fee is usually refunded too. If you refund a $100 payment that cost you $3.20 in fees, you get back the $3.20 as well. Check your transaction history to confirm the refund was processed correctly.

Fees for Different QuickBooks Products

The payment processing fees are the same across QuickBooks Online, QuickBooks Online Plus, and QuickBooks Self-Employed—the rates do not change based on which subscription tier you use. However, some tiers include features that reduce fees in other ways. For example, QuickBooks Online Plus includes unlimited invoices and advanced reporting, which can help you send invoices more efficiently and track payment methods more easily.

If you use QuickBooks Desktop (the older, non-cloud version), payment processing works differently and may require a separate payment processor. Check your QuickBooks Desktop settings or contact QuickBooks support to see which payment methods are available and what fees apply.

When You Might Pay More or Less

Some situations change the fee you pay. If a customer disputes a charge or files a chargeback (tells their bank the charge was unauthorized), QuickBooks may charge you a chargeback fee on top of the original payment fee. This fee is usually $15 to $25 per chargeback and is meant to cover the cost of investigating the dispute. You can reduce chargebacks by keeping clear records of what you sold and when, and by being responsive if a customer questions a charge.

If you process a very large number of payments per month, you may be able to negotiate lower rates with QuickBooks. This is not automatic—you would need to contact QuickBooks sales directly. Most small businesses pay the standard rates.

Frequently Asked Questions

Can I see the fee before I process a payment?

Yes. In QuickBooks Online, when you enter a payment amount and select the payment method, the system shows you the fee and the net amount you will receive. You can see this before you confirm the transaction. This applies to invoices, estimates, and manual payment entries.

Do I have to use QuickBooks Payments, or can I use a different processor?

You can use a different processor if you want. QuickBooks integrates with other payment processors like Stripe and Square. You would set up the integration in your QuickBooks settings, and payments would flow into QuickBooks automatically. The fees would be whatever that processor charges, not QuickBooks rates.

What happens if a customer's bank transfer fails?

If an ACH payment fails (the customer's bank rejects it), QuickBooks usually does not charge you a fee for the failed transaction. However, if the customer tries again and it succeeds, you pay the fee on the successful payment. Check your transaction history to confirm whether a failed payment was charged.

Are QuickBooks payment fees tax deductible?

Yes, payment processing fees are a business expense and can be deducted on your taxes. Keep records of your payment fees (QuickBooks generates reports for this) and include them in your business expense deductions. Talk to a tax professional about how to categorize them on your specific tax return.

Do I pay fees on refunds I issue?

When you refund a payment, the original fee is usually refunded to you as well. So if you charged a customer $100 and paid $3.20 in fees, and then refund the $100, you get the $3.20 back. The refund itself does not cost you an additional fee.