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About QuickBooks Online and Bill Pay

Apr 11th 2019
Share this content offers a bill payment app for QuickBooks Online, called Bill Pay. I recently setup the Bill Pay for QBO app for a client, and had some significant challenges, so I wanted to share my thoughts and personal experience. 


When this app is enabled, you can pay bills inside QBO and will pay the Vendor either via ACH (requires extra setup) or via paper check (higher fee than ACH).

As of this writing, the pricing is: no monthly fee; $0.99 per ACH transaction; $1.99 per check.  For more details, costs, etc. check out the app page description here. Note: there are two levels,  Bill Pay for QBO and Bill Pay for QBO Advanced.


I had setup Bill Pay for another client sometime last year, and don’t recall having any hitches. The most recent setup, however, I have to admit was nothing short of a disaster.

First off, wanted to run a credit check on the client before initializing the Bill Pay account.  On behalf of my client, I entered the answers to the questions, then encountered questions along the lines of “Which of these phone numbers have you been associated with in the past?” and “In which of these counties have you owned real estate?”

Not knowing these answers, I forwarded the questions to my client, but she was unable to reply to me until the following day. When I attempted the process again, there were different questions, which I again had to forward to my client and again it took 24 hours to receive the replies.

By this time, suspected something was up, said the identity check had failed, but not to worry I could mail in some physical paperwork and the account would be setup in no time. Here is the physical paperwork they required:

1.    Valid State/Federal ID or passport, front and back, front page in color.
2.    Company’s most recent bank statement.
3.    Signed copy of the company’s Articles of Incorporation; if Sole Proprietor, business license and EIN certificate.
4.    AND one of the following: Military ID; passport (if not already provided); employer issued ID; utility bill in your name.

These paper docs had to be sent via U.S. Mail, which I was embarrassed to ask my client to do, but she complied based on my recommendation of the use of this app. 

A week after sending all of the documents in, we still had heard nothing back, so I contacted Support. The rep told me the docs had indeed been received (even though we were never notified) and the account was now verified, so I could start paying vendors.

Lesson learned: Don’t try to setup Bill Pay without having the client on standby to answer credit check questions. 

Vendor Setup

The Bill Pay app strongly encourages the QBO account owner to Invite Vendors to the Bill Pay app. Inside the app, there is a vendor list. Locate the vendor you wish to invite and click the blue “Set up bank transfers” link. Bill Pay will send an email invite to the vendor (recommended), or if you have the vendor’s ACH information, you can manually enter it. For most vendors, you will have Bill Pay send the invite.

When the vendor receives the email invite, they are prompted to create a login and then enter their ACH info (bank account number, bank routing number). This is nice, because you/your client never have to request or store this information.

Once the vendor has completed this step, their Vendor record shows they are setup for Bank transfer as the payment method, which is lovely. Most Vendors will truly appreciate receiving payment of their bill via direct deposit. 

My client setup, however, somehow had a glitch. The vendor list and Bank Account list synced to twice. No one could tell me why, so every vendor and primary checking account was duplicated. 

As a result, bills which had already been paid before Bill Pay was even turned on were being marked as Not Paid because the bill for Version 1 of the vendor had been paid. However, the bill for Wersion 2 (aka the duplicate vendor) was showing as Not Paid.

It took an hour long chat session to get this sorted out and the duplicate bank account also took a long time to sort out with the chat rep even going so far as to ask me why I had deleted the primary checking account, which I assured him I had not.

Due to the ongoing problems with the vendor and account duplication, my case had to be escalated to an engineer, which took another few days to sort out.  In the end, all the issues were resolved, but it took over two hours of chat and a one-hour phone call. 

Paying Vendors

Once Vendors are setup for Bill Pay, you use the Bill Pay screen to pay the bills by going to Expenses | Vendors and clicking on a white button called “Pay bills online.” This launches the Bill Pay screen and like the regular bill payment workflow, you can cherry pick the payment account, the bills you want to pay and the amount.

Note: You do NOT go to the vendor record or directly to the bill to use Bill Pay, as this launches the QBO native bill payment screen and there is no option to pay the bill via ACH.

There is also an option to “Send a payment,” presumably to someone you want to pay who has not submitted a bill. I have not used this feature, but it looks promising.

Once you have paid bills via Bill Pay, click on the tab called “Sent Payments” to see the vendor name, bill number, date payment is scheduled to go out, date payment was actually made and the payment amount. There is also a “Track Status” link which provides a reference number. 


Bill Pay sends the account owner’s (my client, not me) an email showing a summary of the bills paid, which is a nice feature. There is also an option to send the vendor a notification that their payment has been processed and is forthcoming, which is also nice.

Bill Pay also periodically sends notification of bills which have not been paid. This seems like a good feature, but I found it plain annoying. I like to enter my client’s phone and utility bills into QBO, even if they are on auto-pay with the vendor, so when the auto-pay is made, it flows through the bank feed and appears as a Match to the bill.

As a result, these bills can sit 10-20 days until the auto-pay is processed, so they keep showing up on the Bill Pay notification email as unpaid bills. Since I will never be using Bill Pay to pay those bills, it is annoying. If there is a way to turn the notifications off, I have yet to locate it.

e-Bill Feature Not Working offers something called e-Bills, described on the website as follows, “Invoice a client who is already using customers can connect through our network to invoice each other and get paid - one company's eInvoice becomes another's eBill, along with all of the data, including attachments and complete with status updates along the way.”

This feature is great if you are using the full version of, but it does not seem to work within Bill Pay for QBO. For the new setup I just completed, one of the vendors already had a account, so she sent an eInvoice and my client received an email notification she had received an eBill.

The vendor’s bill then automagically appeared in the Bill Pay bill payment screen, however, no copy of the bill ever arrived by email or attached to the bill in QBO. I advised my client that we don’t want to pay a bill we’ve never seen, so I asked the vendor not to use the eInvoice feature. Instead, I advised she just email us her bills and we would manually enter them into QBO. 

Other Stuff

There is also a feature to mark bills as paid outside of and I found it once when a support rep led me to it during a chat session, but I could not find it again. In the Bill Pay screen, you can click a bill as if you are going to pay it and then a “Batch Actions” button appears with a drop down with the choices to either “Remove from Bill Pay” or “Delete.” I thought the “Mark bill as paid outside of Bill Pay” option was there too, but I didn't see it.

Here's also something I have yet to figure out: With the Bill Pay client I setup last year, I cannot pay her bills if I am logged in as myself in my QuickBooks Online Accountant (QBOA) account. I have to logout as me, login as my client (and I hate asking my clients for their login credentials), pay the bills she authorized me to pay, then log out as her and log back in to my QBOA account. I hate these extra steps.

However, for the new account I just setup I am able to pay bills she has authorized me to pay when I am logged into my own QBOA. I have no idea what I did differently in the setup to make this happen, I wish it was more clear so I can do it again for the next setup (and fix it for the other client’s setup).


Be careful using Google to find FAQs or support articles for Bill Pay, as most of what you will find is for the full version of  This link provides FAQs specifically for Bill Pay for QuickBooks Online.

A Support button at the top of the Bill Pay screen offers a Video Overview, links to the FAQs noted above and a phone number for Support, which is offered Mon-Fri 6am-6pm & Sat 6am-3pm PST. 


It took me over three weeks to get Bill Pay setup and then it took over three hours of phone and chat support to get it working. Once I passed those hurdles, it was working well. My client likes it, I like that she can pay bills from her login and/or I can pay her bills from my QBOA login. The vendors also love receiving their payments via ACH.

In the end, I do recommend this app and I expect most bookkeepers won’t endure the significant setup challenges I faced. If you are setting up Bill Pay for your client, I strongly recommend you have them on the phone with you or otherwise immediately available to answer all the setup questions so you don’t have to mail in the physical paperwork, which is extremely onerous. If you've used this app, please shafe positive or negative experiences you’ve had as it will only help other users.

Author's Update: I wanted to circle back to report that days after posting my blog article about Bill Pay powered by, I received a message from the company's VP of Product Management. He asked for an opportunity to chat about my experience and how could do better with the Bill Pay product.

We subsequently had that chat and I'm delighted to report that his team is reviewing all the pain points I noted above with the goal of improving the user experience in general, and the setup in particular. Kudos to for listening and responding to user feedback!

Editor's Note: The above review is the viewpoint and experiences of the author and do not necessarily reflect those of AccountingWEB, its parent Sift Media or any of its valued affiliates.

Jody Linick is an AIPB Certified Bookkeeper and a QuickBooks® Certified Pro Advisor.  Her company, FitBooks Pro (formerly called Linick Consulting), specializes in remote bookkeeping services using hosted QuickBooks and QuickBooks Online. You can find her series of Blog posts here.

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