QuickBooks charges between 2.4% and 3.5% plus $0.25 per transaction for credit card payments, depending on which QuickBooks product you use and how you process the card
QuickBooks does not charge a single rate across all its products. The cost depends on whether you process cards through QuickBooks Payments (their own processor), a third-party processor integrated into your account, or manually enter card details. If you use QuickBooks Payments directly, you'll pay a percentage-based fee plus a per-transaction fee. If you use a third-party processor like Stripe or Square integrated with QuickBooks, you pay that processor's rates instead, which may be lower or higher.
The rates also vary by card type. Debit cards, online transactions, and in-person card-present transactions (where you swipe or insert the card) each have different rates. American Express typically costs more than Visa or Mastercard. Understanding which rate applies to your situation matters because the difference between 2.4% and 3.5% on a $1,000 payment is $11 — money that adds up across hundreds of transactions.
Key Takeaways
- QuickBooks Payments charges 2.4% + $0.25 for online card-not-present transactions and 2.7% + $0.25 for in-person card-present transactions, with American Express running higher.
- You can integrate third-party processors like Stripe, Square, or PayPal into QuickBooks and pay their rates instead, which may be cheaper depending on your transaction volume.
- Manually entering card details into QuickBooks invoices does not process the payment through QuickBooks Payments — you must use the integrated payment option or a connected processor.
- Rates do not include monthly subscription fees for QuickBooks itself, which range from $15 to $200+ depending on the product tier.
- QuickBooks Self-Employed and QuickBooks Online do not offer built-in payment processing; you must use a third-party processor or QuickBooks Payments if available in your region.
QuickBooks Payments rates for card-not-present transactions
When a customer enters their card details online — through an invoice link, payment page, or your website — QuickBooks charges 2.4% of the transaction plus $0.25 per transaction. This applies to Visa, Mastercard, and Discover. American Express costs 3.5% plus $0.25. These are the rates as of the most recent update, but QuickBooks has changed rates in the past and may do so again.
The 2.4% rate is competitive for online payments, but the $0.25 per-transaction fee adds up. On a $50 payment, you pay $1.45 total (2.4% + $0.25). On a $500 payment, you pay $12.25. The percentage matters more as transaction size grows, but the flat fee hurts on small payments.
QuickBooks Payments rates for card-present transactions
If you swipe, insert, or tap a physical card using a QuickBooks card reader, the rate is 2.7% plus $0.25 for Visa, Mastercard, and Discover. American Express is 3.5% plus $0.25. Card-present transactions cost slightly more than card-not-present because the fraud risk is lower (the card holder is physically present), but QuickBooks passes a higher interchange rate to you.
You need a compatible card reader to process in-person payments. QuickBooks sells or partners with hardware providers, and the reader cost is separate from the per-transaction fee. Some readers are free with a QuickBooks subscription; others cost $20 to $100 depending on the model.
How third-party processors change the cost
QuickBooks Online integrates with Stripe, Square, PayPal, and other processors. When you connect one of these, you pay that processor's rates, not QuickBooks Payments rates. Stripe charges 2.9% + $0.30 for online transactions. Square charges 2.6% + $0.10 for online and 2.6% + $0.10 for in-person. PayPal charges 2.2% + $0.30 for online payments.
Switching processors can save money. If you process $10,000 in online transactions per month, QuickBooks Payments costs you $240 + $2.50 = $242.50. Stripe costs $290 + $3 = $293. Square costs $260 + $1 = $261. PayPal costs $220 + $3 = $223. The difference is small on this volume, but at $50,000 per month, it becomes significant. Compare the rates for your actual transaction size and mix before choosing.
Not all QuickBooks products support all processors. QuickBooks Self-Employed does not integrate with any processor; you must use a standalone payment tool. QuickBooks Online Plus supports more integrations than QuickBooks Online Essentials. Check the product documentation for your specific version.
What is not included in QuickBooks payment fees
The per-transaction fees above do not include your QuickBooks subscription. QuickBooks Online Essentials costs $15 per month. QuickBooks Online Plus costs $90 per month. QuickBooks Self-Employed costs $15 per month. These are separate from payment processing fees. You pay both.
ACH bank transfers (moving money from a customer's checking account) have different fees. QuickBooks charges 1% of the transaction amount with a $0.25 minimum and $10 maximum per transaction. This is cheaper than credit cards for large payments but slower — ACH takes three to five business days.
International card processing, if available in your region, may have additional fees. Chargeback fees (when a customer disputes a transaction) are typically $15 to $25 per chargeback, charged by the processor, not QuickBooks directly.
How to see your actual QuickBooks payment costs
Log into QuickBooks Online and go to Settings > Account and Settings > Payments. You will see which processor is connected and the current rates. If you use QuickBooks Payments, the rates display there. If you use a third-party processor, the rates shown are that processor's rates, not QuickBooks'.
Your transaction history shows the fee deducted from each payment. Open Transactions > Customers > Invoices, find a paid invoice, and click the payment. The fee appears as a line item. Over time, you can calculate your average cost per transaction by dividing total fees by total transactions processed.
If you are comparing processors, create a spreadsheet with your typical transaction sizes and mix (how many $50 transactions, how many $500 transactions, etc.). Calculate the total fee for each processor using their rates. The processor with the lowest total cost for your actual pattern is the best choice, not the one with the lowest advertised rate.
Frequently Asked Questions
Does QuickBooks charge a fee if I manually enter a credit card number into an invoice?
No. Manually typing a card number into an invoice does not process the payment through QuickBooks. You must click the payment button or use an integrated processor to trigger the fee. If you manually enter the card and process it outside QuickBooks (through your bank or a separate payment tool), QuickBooks charges nothing — but you lose the automatic reconciliation benefit.
Can I use my own payment processor instead of QuickBooks Payments?
Yes, if you use QuickBooks Online. You can integrate Stripe, Square, PayPal, or other processors and pay their rates instead. QuickBooks Self-Employed does not support integrations, so you must use a standalone processor and manually record payments in QuickBooks. Desktop versions of QuickBooks do not have built-in payment processing at all.
What happens if a customer's card is declined?
QuickBooks does not charge a fee for declined transactions. The payment straightforward fails, and the invoice remains unpaid. The customer can try again with a different card or payment method. You can resend the invoice link or contact them to collect payment another way.
Are QuickBooks payment fees tax-deductible?
Yes, payment processing fees are a business expense and deductible on your tax return. Keep records of your monthly processing fees (QuickBooks provides a summary in your account settings) and report them as a business expense. Consult a tax professional for your specific situation.
Do I pay the same rate for all card types?
No. American Express costs more than Visa or Mastercard with QuickBooks Payments. Debit cards may have different rates depending on whether they are signature debit or PIN debit. Check your processor's rate card for the exact breakdown by card type.