QuickBooks is the accounting software behind millions of small and mid-sized businesses. But accounting is only half the picture — you also need a reliable way to collect payments. QuickBooks Payments is Intuit's built-in payment processing solution that lets you accept credit cards, ACH bank transfers, and digital wallets directly inside QuickBooks Online.
For many businesses, accepting payments through QuickBooks is the simplest path to getting paid faster. Customers can pay invoices with a single click, and every transaction automatically syncs to your books. But QuickBooks Payments is not the right fit for every scenario — especially if you need advanced gateway features, multi-currency support, or custom checkout flows.
This guide walks through everything you need to know: how to set up QuickBooks Payments, how to accept online payments on invoices and your website, what it costs, and when a third-party gateway is the better choice.
What Is QuickBooks Payments?
QuickBooks Payments is the payment processing feature built into QuickBooks Online. It allows businesses to accept credit card payments, debit card payments, and ACH bank transfers directly through invoices, sales receipts, and online checkout links — without needing a separate merchant account or payment gateway.
When a customer pays an invoice, the money flows through Intuit's payment processing infrastructure and deposits into your linked bank account. The transaction is automatically recorded in QuickBooks, which eliminates manual reconciliation and reduces errors.
This is an example of embedded payments — payment processing built directly into the software you already use, rather than bolted on as a separate tool. The benefit is simplicity: one login, one dashboard, and automatic bookkeeping.
QuickBooks Payments supports the following payment methods:
Credit and debit cards — Visa, Mastercard, American Express, and Discover
ACH bank transfers — direct debit from the customer's bank account at a lower fee
Apple Pay — available on supported mobile invoices and online checkout pages
PayPal and Venmo — optional add-on for invoice payments (US only)
How to Set Up QuickBooks Payments
Setting up QuickBooks Payments takes about 10 minutes if you already have a QuickBooks Online subscription. Here is the step-by-step process:
Step 1: Sign in to QuickBooks Online. Go to Settings (gear icon) and select Account and Settings.
Step 2: Navigate to Payments. In the left sidebar, click Payments. If you have not set up QuickBooks Payments before, you will see an option to "Learn how you can accept online payments."
Step 3: Complete the application. Intuit will ask for your business type, legal name, EIN or SSN, business address, and bank account for deposits. Sole proprietors can use their personal SSN.
Step 4: Verify your identity. Intuit may request additional documents for verification. Most applications are approved within one business day.
Step 5: Configure deposit settings. Choose between standard deposits (next business day, free) or same-day deposits (1% fee, up to $25 per deposit). Link the bank account where you want funds deposited.
Once approved, QuickBooks automatically adds a "Pay now" button to your invoices. You can also enable payment reminders to nudge customers who have not paid.
Accepting Payments on QuickBooks Invoices
The most common way to accept online payments in QuickBooks is through invoices. When you send an invoice with QuickBooks Payments enabled, the customer receives an email with a "Review and pay" button that opens a secure payment page.
Here is how to configure invoice payments:
Choose accepted payment methods. When creating an invoice, you will see checkboxes for credit/debit cards, ACH bank transfer, and PayPal/Venmo. You can enable or disable methods per invoice.
Set default payment methods. In Account and Settings > Payments, choose which methods are enabled by default on every invoice so you do not have to configure each one manually.
Enable payment reminders. QuickBooks can send automatic reminders before, on, and after the due date. This significantly improves collection rates — Intuit reports that businesses using automatic reminders get paid up to twice as fast.
Track payment status. The invoice dashboard shows which invoices are open, overdue, or paid. Once a customer pays, the invoice is automatically marked as paid and the payment is recorded in your general ledger.
For businesses that send a high volume of invoices and want deeper customisation of the payment experience, integrating a third-party gateway can offer more flexibility. See our guide on maximising invoice payments with Stripe or maximising invoice payments with Authorize.net for alternatives.
Accepting QuickBooks Payments on Your Website
QuickBooks Payments is not limited to invoices. You can also accept payments on your website using QuickBooks' online checkout features:
Payment Links
QuickBooks lets you create shareable payment links for specific products or services. Embed them on your website, share in emails, or post on social media. Each link opens a hosted checkout page where customers enter their payment details, and the transaction records automatically in QuickBooks.
Payment links are a fast way to collect payments online without a full ecommerce checkout. However, customisation is limited — you cannot change the checkout page design, add custom fields, or create multi-step flows.
QuickBooks Online Store
Intuit offers a basic online store feature for QuickBooks Commerce subscribers. This gives you a product catalogue and checkout experience, but it is basic compared to dedicated ecommerce platforms like Shopify or WooCommerce. It works best for service-based businesses that sell a small number of items.
QuickBooks API for Custom Integrations
For businesses with custom websites or SaaS platforms, the QuickBooks Payments API allows you to process payments programmatically and sync transactions to QuickBooks. This requires development resources but gives you full control over the payment experience while keeping your accounting data in sync.
QuickBooks Payments Fees and Pricing
QuickBooks Payments pricing is straightforward — there is no monthly fee for the payment processing feature itself (you only need a QuickBooks Online subscription). Fees are charged per transaction:
Invoice payments (card): 2.99% per transaction
Invoice payments (ACH/bank transfer): 1% per transaction ($1 minimum)
Online checkout / payment links (card): 2.99% per transaction
In-person / card reader: 2.5% per transaction
Same-day deposits: 1% per deposit (maximum $25)
Compared to standalone gateways, QuickBooks Payments pricing is competitive for invoice-based businesses. The 2.99% card rate is slightly higher than Stripe's 2.9% + 30 cents, but the absence of a per-transaction fixed fee benefits businesses processing smaller transactions. ACH at 1% is significantly cheaper than card payments and worth encouraging customers to use.
Keep in mind that you need a QuickBooks Online subscription ($35-$235/month depending on tier) to use QuickBooks Payments. If you are only looking for payment processing and do not need accounting software, a standalone gateway may be more cost-effective.
QuickBooks Payments vs Third-Party Gateways
QuickBooks Payments works well for straightforward payment collection, but it is not a full-featured payment gateway. Here is how it compares to popular third-party options:
QuickBooks Payments vs Stripe
Stripe is a developer-first payment platform for businesses that need custom checkout experiences, subscription billing, and multi-currency support. Stripe supports 135+ currencies and dozens of local payment methods. QuickBooks Payments only supports USD.
Choose Stripe if: you sell internationally, need subscription billing, want a custom checkout experience, or are building a platform that needs to route payments to multiple parties.
Choose QuickBooks Payments if: you primarily invoice US-based customers, want the simplest possible setup, and value automatic accounting reconciliation over customisation.
QuickBooks Payments vs Authorize.net
Authorize.net is a traditional payment gateway that integrates with hundreds of shopping carts, CRMs, and business tools. It supports recurring billing, a fraud detection suite (AFDS), and customer payment profiles for card-on-file transactions. For more detail, see our guide on payment links for Authorize.net.
Choose Authorize.net if: you need a standalone gateway with broad integration support, advanced fraud tools, or need to process through a specific merchant account provider.
Choose QuickBooks Payments if: you want a zero-setup solution that lives inside your accounting software and do not need advanced gateway features.
When to Use Both
Many businesses use QuickBooks Payments for invoice collection while running a third-party gateway for their website or app. Stripe and Authorize.net both have QuickBooks integrations that sync transactions into your books — giving you a powerful gateway for online sales and frictionless invoice payments.
Limitations of QuickBooks Payments
QuickBooks Payments is convenient, but it has notable limitations that may push growing businesses toward dedicated payment platforms:
US only. QuickBooks Payments is only available to US-based businesses and only processes transactions in USD. If you have international customers or need multi-currency support, you will need a different gateway.
Limited payment methods. No support for local payment methods like iDEAL, SEPA Direct Debit, Klarna, or Afterpay. Digital wallet support is limited to Apple Pay.
No subscription billing. QuickBooks has recurring invoices, but there is no built-in subscription management with dunning, proration, plan changes, or usage-based billing.
Basic fraud tools. QuickBooks Payments does not offer configurable fraud rules, 3D Secure authentication, or risk scoring. High-risk or high-volume merchants may need more robust fraud prevention.
Minimal checkout customisation. The hosted payment pages and invoice checkout cannot be branded or customised beyond basic logo and colour settings.
Platform and marketplace limitations. QuickBooks Payments does not support split payments, connected accounts, or multi-party payment flows that platforms and marketplaces require.
Using Payment Links with QuickBooks
Payment links are one of the fastest ways to collect payments without building a full checkout. QuickBooks offers its own payment links feature, but you can also use third-party payment link providers for more flexibility.
QuickBooks payment links let you create a shareable URL for a fixed amount or a product. Customers click the link, enter their payment details on a hosted page, and the payment records automatically in QuickBooks. They work well for simple use cases: collecting deposits, one-off service fees, or event registrations.
For more advanced scenarios — like branded checkout pages, custom fields, multi-currency payments, or connecting payment collection into automated workflows — third-party payment links from providers like Stripe or Authorize.net can be integrated with QuickBooks via apps or middleware.
If you are a platform or SaaS company that integrates with QuickBooks and needs to offer payment collection to your users, Shuttle provides payment link infrastructure that can connect to QuickBooks workflows. Rather than building and maintaining payment integrations yourself, you can embed payment links into your platform and let Shuttle handle the payment processing, PCI compliance, and gateway orchestration.
Tips to Get Paid Faster with QuickBooks Payments
Enabling QuickBooks Payments is only the first step. These practices help you reduce days sales outstanding (DSO) and improve cash flow:
Enable ACH payments. Many customers prefer bank transfers, especially for larger invoices. The lower fee (1% vs 2.99%) also saves you money.
Turn on automatic reminders. Set reminders for 7 days before, on the due date, and 7 days after. QuickBooks handles the emails so you do not have to chase payments manually.
Offer multiple payment methods. The more options you give customers, the fewer excuses they have to delay. Enable cards, ACH, and Apple Pay on every invoice.
Send invoices immediately. Do not wait until month-end. Send invoices as soon as work is completed or products are delivered. QuickBooks makes it easy to invoice from your phone.
Use payment links for non-invoice payments. For deposits, retainers, or one-time charges, send a payment link instead of a full invoice. It is faster for both you and the customer.
Frequently Asked Questions
How much does QuickBooks Payments cost?
There is no additional monthly fee for QuickBooks Payments beyond your QuickBooks Online subscription. You pay per transaction: 2.99% for card payments on invoices and online checkout, 1% for ACH bank transfers ($1 minimum), and 2.5% for in-person card reader transactions. Same-day deposits cost an additional 1% per deposit, capped at $25.
Can I accept payments through QuickBooks without a website?
Yes. QuickBooks Payments works primarily through emailed invoices. When you send an invoice, your customer receives an email with a secure "Pay now" link — no website required. You can also create standalone payment links to share via email, text message, or social media.
Does QuickBooks Payments work outside the United States?
No. QuickBooks Payments is only available to US-based businesses and processes transactions in USD only. If you need to accept international payments or multiple currencies, you will need a third-party gateway like Stripe.
Can I use Stripe or Authorize.net with QuickBooks?
Yes. Both Stripe and Authorize.net offer QuickBooks integrations that sync payment data into your accounting. You can use a third-party gateway for your website or app checkout while using QuickBooks Payments for invoice collection, or use the third-party gateway exclusively and sync everything to QuickBooks for bookkeeping.
How long does it take to receive QuickBooks Payments deposits?
Standard deposits arrive the next business day at no extra cost. Same-day deposits are available for a 1% fee (maximum $25 per deposit). ACH bank transfer payments take 5-7 business days to process before the funds are deposited.
Next Steps
For most small businesses using QuickBooks Online, enabling QuickBooks Payments is a no-brainer. It takes minutes to set up, costs nothing extra per month, and gets invoices paid significantly faster.
If you need more than what QuickBooks Payments offers — international payments, advanced fraud detection, subscription billing, or custom checkout flows — explore a third-party gateway like Stripe or Authorize.net and integrate it with your QuickBooks account.
And if you are a platform or SaaS company that needs to offer payment collection to your users alongside QuickBooks, book a discovery call with Shuttle to learn how embedded payment links and gateway orchestration can plug into your existing workflows.