QuickBooks Online Invoicing With Flexible Pay Later Options

Sponsored Content. By Intuit QuickBooks x Affirm.

For owners of small and mid-sized companies, cash flow is a living, daily concern—not a static cell in a spreadsheet. When payments land as expected, operations move smoothly; when they slip, even brief lags can strain payroll, inventory, and routine workflows.

Delays, unfortunately, are common in day-to-day business.

Intuit’s Small Business Late Payments Report finds that 56% of small firms are waiting on unpaid invoices, with an average of $17,500 outstanding per business. Nearly half say some invoices are more than 30 days late. That backlog isn’t abstract—it forces difficult choices about which bills get covered first.

The stretch between finishing work and receiving funds creates real pressure. In a separate Intuit survey, 39% of business owners said a single overdue payment jeopardized their ability to make payroll or pay essential bills.

Customers often intend to pay, but rising costs and broader economic headwinds can disrupt timing. That leaves businesses waiting on revenue they’ve already earned and forecasted.

Why Traditional Invoices Create Friction

Many invoicing tools haven’t kept pace with customer expectations. Standard invoices typically demand the full amount upfront and offer few payment method choices, which adds friction when a client needs a payment plan or installment flexibility.

When payment options are narrow, late payments become more likely—not from unwillingness, but because timing doesn’t align. The result is a longer gap between delivery and when you get paid, pushing owners to bridge the shortfall with other short-term funding options or internal reserves.

QuickBooks can accept partial payments on an invoice in the normal “Receive payment” flow, leaving the remaining balance open until it’s paid. For installment-like arrangements without a third-party pay-over-time option, businesses typically handle it operationally (for example, by collecting a deposit and then billing the remainder later), rather than relying on a built-in consumer installment plan on a single invoice.

Putting Pay Over Time Inside QuickBooks Payments

Intuit and Affirm have partnered to bring Affirm’s buy now, pay later option directly into the QuickBooks Payments experience (1). Eligible businesses can let customers split an invoice into installments alongside card or bank transfer, at accessible rates, right from the invoice.

For customers, the pay-over-time choice appears during invoice payment alongside other methods. If they select it, they complete a short Affirm checkout that includes an eligibility check and, when approved, choose from available installment terms before confirming payment.

For businesses, this requires using QuickBooks Payments and meeting eligibility requirements; availability can vary, and some accounts may need to request access (1). Once enabled, payments made through this option are processed through QuickBooks Payments, the invoice is marked as paid, and the transaction is recorded and reconciled in QuickBooks Online like other payment activity—reducing manual work and helping cash flow move faster.

When a customer chooses this route, the business gets paid upfront (2), while the customer pays Affirm over time. Because repayment happens between the customer and Affirm, the repayment risk is generally handled by Affirm rather than the business, though standard payment processing considerations can still apply (including fees and the operational handling of refunds or disputes).

At this time, QuickBooks Payments supports Affirm as the integrated pay-over-time option described here; it does not offer the same built-in invoice option for Afterpay, Klarna, Zip, or Sezzle.

Whether pay over time affects a customer’s credit can depend on the lender, the specific plan offered at checkout, and the customer’s payment behavior. Customers see any applicable disclosures during the Affirm checkout, and missed payments may affect a customer’s credit depending on the terms of the loan.

To turn the pay-over-time option on or off for invoices, follow these steps in QuickBooks Online:

1. Sign in to QuickBooks Online as an admin for the company.
2. Open Settings, then select Account and settings.
3. Select the Payments section.
4. Find the pay-over-time setting for Affirm and toggle it on or off.
5. Select Save, then confirm the setting is available on new invoices you send.

Offering pay-over-time at the point of invoice can shorten the distance between completed work and usable cash, especially when customers need flexibility but the business still needs predictable inflows.

What This Means for Small and Mid-Market Businesses

The difference between being paid today and weeks from now is substantial. With pay over time integrated into QuickBooks Payments, you can offer more ways to pay while still getting funds upfront, helping stabilize cash flow instead of constantly catching up.

More than half of small businesses say cash flow isn’t an issue when invoices are paid upon receipt (3).

• Increase on-time payments.
• Improve cash flow predictability.
• Reduce reliance on credit.
• Cut time spent chasing late invoices.
• Support confident business decisions.

It’s also worth weighing potential downsides, including processing costs, the possibility that some customers won’t qualify at checkout, and added complexity when handling refunds or disputed transactions. And while the business may be paid upfront, customer experience can still be affected if a buyer is declined or chooses a different method at the last moment.

By building flexibility into how customers pay, businesses gain another lever to keep revenue moving without adding operational complexity.

A Small Shift With Meaningful Impact

Flexible payment choices won’t erase every late payment. But for many firms—especially those issuing larger invoices or billing by project—they can reduce a major source of uncertainty. This also reflects a broader mindset shift: invoicing is no longer a back-office afterthought. It’s part of the customer experience and a tool to improve financial outcomes.

Some certified public accountants prefer not to use QuickBooks Online for certain clients due to factors like differences from long-familiar desktop workflows, occasional syncing or bank feed troubleshooting, limitations in certain reporting or customization needs, and the realities of an always-online, subscription-based system. Others prefer it for collaboration and automation, but the friction usually comes down to workflow preferences and control expectations.

QuickBooks Desktop is not automatically “discontinued in 2026” as a blanket product status. However, specific Desktop versions and offerings can be changed or retired over time, and support for older versions can end on a scheduled cycle—so the practical answer depends on which Desktop edition and version a business is using.

As more companies seek steadier cash flow and clearer planning, offering pay later and other flexible options is quickly becoming the norm for both businesses and customers.

Money movement services are provided by Intuit Payments Inc., licensed as a Money Transmitter by the New York State Department of Financial Services. Payment options through Affirm are provided by Affirm’s lending partners (see /lenders).

Options depend on purchase amount, and a down payment may be required. Availability and eligibility can vary. Restrictions apply. See /terms#use and /licenses.

(0) Money movement services are provided by Intuit Payments Inc., licensed as a Money Transmitter by the New York State Department of Financial Services. For details about money transmission licenses, or for Texas customers with complaints, visit /legal/licenses/payment-licenses/.

(1) Payment options through Affirm are subject to an eligibility check, may not be available everywhere, and are provided by Affirm’s lending partners at /lenders. Example: $1,000 could cost $90.26 per month over 12 months at 15% interest rate. Options depend on the amount, and a down payment may be required. Licenses and disclosures: /licenses. Buy now, pay later features have limited availability and may change. If you do not see Affirm in your QuickBooks Online account, email [email protected] to request access.

(2) Payment timing is subject to standard processing fees.

(3) Based on the 2025 Intuit QuickBooks Late Payments Report.