QuickBooks Payments is a payment processor built into QuickBooks accounting software

QuickBooks Payments lets you accept credit cards, debit cards, and bank transfers directly from your QuickBooks invoices and point-of-sale system. Instead of using a separate payment processor, the tool sits inside the accounting software you already use, so payments land in your QuickBooks records automatically without manual entry.

The service is run by Intuit, the company that makes QuickBooks. It connects to your business bank account and processes the transaction, then deposits the money minus a processing fee. Because it's built into QuickBooks rather than bolted on top, it reduces the steps between a customer paying you and that payment showing up in your accounting ledger.

You don't have to use QuickBooks Payments if you have QuickBooks — you can connect other processors like Stripe or Square instead. But if you're already paying for QuickBooks, adding Payments means fewer logins and fewer places to track what customers owe you.

Key Takeaways

  • QuickBooks Payments processes credit cards, debit cards, and ACH bank transfers and deposits the funds into your business bank account.
  • Payments you receive through the system show up automatically in your QuickBooks ledger, so you don't have to enter them by hand.
  • You can send payment links through invoices, accept payments at a physical location with a card reader, or embed a payment button on your website.
  • QuickBooks Payments charges a percentage of each transaction plus a per-transaction fee, and the exact rate depends on your QuickBooks plan and the payment method.
  • If you use a different accounting software or prefer another processor, you can connect Stripe, Square, or other third-party payment systems to QuickBooks instead.

How payments flow from your customer to your bank account

When a customer pays through QuickBooks Payments, the transaction goes through Intuit's payment network, not directly to your bank. Intuit holds the money briefly, deducts the processing fee, and then deposits the remainder into your business bank account — usually within one to two business days.

The customer sees a payment screen that asks for their card details, billing address, and sometimes a phone number. They don't see Intuit's name; they see your business name. Once the payment clears, QuickBooks records it as income in your accounting records and marks the invoice as paid.

This automatic recording is the main reason to use QuickBooks Payments instead of a standalone processor. With a separate payment processor, you'd have to log into that processor, see the payment came in, then log into QuickBooks and manually record it. With Payments, that step is gone.

The three ways to collect payments

QuickBooks Payments works in three different scenarios depending on how your business operates.

Invoice payments: You send a customer an invoice through QuickBooks. The invoice includes a "Pay Now" button. The customer clicks it, enters their payment details, and the money arrives in your account. This works for service businesses, consultants, and any business that bills after work is done.

In-person payments: You use a small card reader that plugs into your phone or tablet. A customer hands you their card, you swipe or tap it, and the payment processes on the spot. This requires the QuickBooks Point of Sale plan and works for retail shops, food trucks, and service businesses that collect payment on-site.

Online store payments: You embed a payment button or form on your website. Customers enter their details and check out without leaving your site. This works if you sell products online and want to avoid sending invoices for every order.

What QuickBooks Payments costs

QuickBooks Payments charges a percentage of the transaction amount plus a flat per-transaction fee. The exact rate varies by payment method and by which QuickBooks plan you use. Credit and debit cards typically cost between 2.4% and 3.5% plus 30 cents per transaction. ACH bank transfers (where a customer pays directly from their checking account) usually cost 1% plus 25 cents, with a cap of $5 per transaction.

These fees are deducted before the money reaches your bank account. If a customer pays you $100 by credit card and the rate is 2.9% plus 30 cents, you receive $96.71 in your bank account.

Some QuickBooks plans include a certain number of free transactions per month before fees kick in. Check your specific plan to see whether you have any free transactions included. If you process a very high volume of payments, Intuit offers custom pricing — you'd need to contact their sales team for a quote.

How QuickBooks Payments connects to your accounting records

When a payment arrives, QuickBooks automatically records it in two places: it marks the invoice as paid, and it deposits the net amount (after fees) into your bank account register. This means your accounting records stay in sync with your actual bank balance without you having to do anything.

The processing fees show up as a separate expense in your accounting records, usually in a category called "Payment Processing Fees" or "Merchant Fees." This is important for tax purposes — you can deduct these fees as a business expense.

If a customer disputes a charge or requests a refund, you can process that refund directly from QuickBooks. The refund goes back to the customer's original payment method, and QuickBooks reverses the original transaction in your records.

When QuickBooks Payments might not be the right choice

QuickBooks Payments works well if you're already using QuickBooks and want a straightforward, integrated solution. But it's not the only option, and it's not always the cheapest.

If you use accounting software other than QuickBooks — such as Xero, FreshBooks, or Wave — you can't use QuickBooks Payments. You'd need to connect a processor that works with your software, like Stripe or Square.

If you process a very high volume of payments, you might negotiate lower rates with a processor that specializes in high-volume merchants. If you have specific payment needs — like accepting cryptocurrency, or collecting payments in multiple countries — you might find a specialized processor that does that better than QuickBooks Payments.

If you want to avoid monthly subscription costs, some standalone processors like Square charge no monthly fee and only take a percentage of each transaction. QuickBooks Payments is included with your QuickBooks subscription, so you're already paying for it whether you use it or not.

Setting up QuickBooks Payments for the first time

To use QuickBooks Payments, you need a QuickBooks Online subscription (the desktop version doesn't support it). You'll connect your business bank account so Intuit knows where to deposit the money. You'll also provide your business tax ID and some basic information about your business.

Once your account is set up, you can start accepting payments when ready. For invoice payments, you just send an invoice as normal — the "Pay Now" button appears automatically. For in-person payments, you'll need to purchase a card reader (usually $30 to $50 depending on the model). For online payments, you'll copy a payment button code into your website.

The setup usually takes less than 15 minutes. If you run into trouble, QuickBooks has phone support available during business hours, and there are step-by-step guides in the QuickBooks help center.

Frequently Asked Questions

Can I use QuickBooks Payments if I have a different accounting software?

No. QuickBooks Payments only works with QuickBooks Online. If you use Xero, FreshBooks, Wave, or another accounting system, you'll need to connect a different processor like Stripe, Square, or PayPal. Some of those processors integrate with multiple accounting platforms.

What happens if a customer's card is declined?

The payment doesn't go through, and the customer sees an error message. QuickBooks doesn't charge you a fee for a declined card. The customer can try again with a different card, or you can send them a new payment link to try later.

How long does it take for money to show up in my bank account?

Most payments deposit within one to two business days. Weekends and holidays can add time. You can see the payment in your QuickBooks records when ready, but the actual bank deposit may take longer.

Can I refund a customer if they change their mind?

Yes. You can process a refund directly from QuickBooks, and the money goes back to the customer's original payment method. The refund usually takes the same amount of time as the original deposit — one to two business days.

Do I pay the processing fee even if a customer's payment fails?

No. You only pay the processing fee if the payment goes through successfully. Declined cards and failed transactions don't cost you anything.