Late fees can be a great tool to encourage positive payment behavior. With QuickBooks online, you can add and set up automatic late fees, choosing when to apply the fee, and the amount. QuickBooks Online features different fee options, such as a flat fee, a percentage, or both.

How to set up late fees

  1. Select Settings ⚙️, then Account and Settings.
  2. From the Menu ☰, select Sales.
  3. Choose Late fees. Check the box to turn on late fees.

Once applied, late fees appear as a separate line item.

(You must be the Master Administrator or the Company Administrator to apply late fees)

Late Fees

QuickBooks Online provides you with 3 different fee types, which you can apply to an invoice:

  • Percentage: charge a specific percentage of the invoice total.
  • Flat Fee: charge a specific amount of your choosing.
  • Percentage & Flat Fee: a combination of both fee types, you can charge a specific amount when the invoice becomes overdue and charge a flat fee if it remains overdue after a set date.


QuickBooks Online allows you to charge different late fee rules to different customers.

  1. From the left menu, select Sales or Invoicing.
  2. Select Customers.
  3. Choose the customer you would like to customize. Then select Late Fees from the table. Here you can choose to waive late fees for a particular customer, or override the default settings and choose your own.

*QuickBooks Online will not automatically send out the updated invoice. You would have to manually send the updated invoice. Alternately, your customer can view the updated invoice online.

Biller Genie Late Fee Manager

Late fees can create payment friction with clients, if proper communication is not established about penalties for late payments. Biller Genie’s Late Fee Manager automatically notifies your customers of the penalties associated with late payments, ensuring proper communication and positive payment behavior. Set your terms and conditions and they will be attached to your outgoing invoice, with the amount you choose, at your preferred frequency.

Biller Genie

Overdue invoices negatively affect cash flow. A U.S. Bank study found that 82% of businesses fail due to cash flow problems. Biller Genie solves this problem. We’re a cloud-based solution that automates accounts receivable from bill presentment, to follow up, and collection – without changing your current process. The Genie does all the heavy lifting for you. It’s simple and The Genie’s magic results in the average small business owner seeing a reduction in outstanding balances by 40 percent. In other words, our subscribers get 40 percent more of their invoices paid than those who don’t use Biller Genie. Small- to medium-sized businesses using Biller Genie also get paid up to 15 days faster. Biller Genie accounts receivable automation software takes the headaches away that are associated with frustrating problems with accounts receivable. Find out what Biller Genie can do for you.