Bill & Pay for QuickBooks Invoicing and Payments

Written by Charlie Russell

The ability to send electronic invoices from QuickBooks and collect payments online is an important feature for many businesses. Let’s take a look at a flexible service that works with both QuickBooks desktop and QuickBooks Online: Bill & Pay.

Payment Processing in QuickBooks

I’m going to focus on QuickBooks desktop in this article, although Bill & Pay also works with QuickBooks Online.

Sending invoices to customers from QuickBooks “electronically” is a simple task, really. All you have to do is to Send the invoice and QuickBooks (if set up properly) will attach a PDF copy of the invoice to an email message that is sent to the customer. Simple!

Although that is a simple enough chore, nowadays there are many ways that you can enhance the process to improve collection rates, shorten the time that a customer takes to make a payment, and automate the collection process for your staff. For example:

  • You can add a link in the invoice to an online payment portal that makes it easier for the customer to make a payment.
  • You can offer your customer multiple ways of making a payment (ACH, PayPal, Credit Card) so that they can choose the method that they prefer.
  • You can automate the process of sending recurring invoices so that you don’t have to manually issue them each month.
  • You can automate the collection process to send reminder emails for nearly due and overdue invoices.

These are some of the benefits that you can get from a comprehensive electronic invoicing and payment processing system. You want to make it easy for the customer to pay, make it easy for your staff to issue the invoices, and provide features to manage payments so that they come in sooner.

Intuit has offered several different kinds of payment processing services that work with QuickBooks, but starting with the release of QuickBooks 2015 this all started to change. They discontinued some of their existing payment systems (such as QuickBooks Billing Solutions) and disconnected QuickBooks from others (Intuit PaymentNetwork), and replaced them with QuickBooks Payments. The transition hasn’t always been smooth for some businesses. Some of the issues have been that the initial releases of QuickBooks Payments had a few problems (many have been fixed by now) and the “feature set” isn’t as full as some people would like (missing some features that existed in the discontinued services). Intuit is committed to fixing problems and adding new features, but at least initially the service seems to be a “lite” version, and many people are looking for something more full-featured.

That is where Bill & Pay comes in.

QuickBooks Payments Using Bill & Pay

Bill & Pay is a comprehensive electronic invoicing and payment processing service that works with QuickBooks desktop and QuickBooks Online. It was recognized as an Awesome App in Sleetercon 2011 and 2012. Once you sit down and play with it you can see why it is truly awesome.

The basic premise is that with Bill & Pay you can create your invoice in QuickBooks as you normally would, and the service will then create an email that it sends to your customer. The invoice can be attached as a PDF file. The email contains a link that takes the customer to your branded portal where they can make a payment and see a history of past transactions. The payment is then posted to your QuickBooks account.

I can’t cover all of the features that the service provides, so here is a list of some of the key features that I’ve come across, and then I’ll jump into the program to show you some of these features. Note that there is a free 30-day trial that you can use to test the features yourself, which I highly recommend that you do.


    • The invoice email is very customizable and will include a link to a payment portal.
    • You can customize the email message sent with invoices to add your customized text and your logo.
    • Emails are sent via the Bill & Pay email server. This simplifies some of the issues that people often run into with QuickBooks and how it integrates with their own email systems.
    • You can use your own domain name for sending email through their system, which is important to some users. Normally the email will come from “[email protected],” with a reference to your email address. Some customers might not accept that for a variety of reasons. To use this feature you have to make some changes to your DNS records, and that can be a complicated process if you aren’t familiar with that kind of thing. For a $50 fee (very reasonable), Bill & Pay customer support can handle the setup for you, although you have to provide them with your domain DNS login information.


  • The payment portal can be branded with your logo and name.
  • Bill & Pay can work with any merchant account, as well as many payment processing gateways such as QuickBooks Merchant Services, Authorize.net, PayPal, BluePay and many more.
  • Payments can be made by credit card or ACH payments.
  • Bill & Pay supports automatic recurring payments, where you can set up a schedule of your choice. Bill & Pay will send the customer an email when their credit card is about to expire if the customer has approved auto-pay. In addition to recurring payments, payment plans are also supported.
  • Customers can view their payment history in the online portal, not just make a payment to the current invoice.
  • When a customer makes a payment in the payment portal, the invoice is marked as “paid” in QuickBooks. This is an important difference from QuickBooks Payments, which only marks invoices as “paid” when the payment clears the bank, which can take several additional days.
  • Bill & Pay can accept payments without an invoice, and will either create a sales receipt or an unapplied credit.
  • There are options for reminder emails to be automatically sent for payments almost due and overdue.

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About the author

Charlie Russell

Charlie Russell has been involved with the small business software industry since the mid 70's, and remembers releasing his first commercial accounting software product when you had an 8-bit microcomputer with one 8 inch floppy disk drive. He has a special interest in inventory and manufacturing software for small businesses. Charlie is a Certified Advanced QuickBooks ProAdvisor with additional certifications for QuickBooks Online and QuickBooks Enterprise, as well as being a Xero Certified Partner. Charlie started blogging about QuickBooks in 2008 (Practical QuickBooks) and has been writing for the Accountex Report (formerly the Sleeter Report) since 2011. He retired from accounting and QuickBooks activities in early 2018.

Visit his CCRSoftware web site for information about his QuickBooks add-on products. He is also the author of the California Wildflower Hikes blog.


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