My first and only client that has ever used QBO bill pay services started in September 2025. The rest of my clients use bill.com. Here are the issues I have found with QBO bill pay:

Bill services needs at minimum an alert that goes out when a shipped check is not delivered/cashed after a period of time. I am just now finding out that a paper check that was due to arrive to the vendor 12/01/25 still shows the status as "shipped". The solution presented was to void and reissue the check. Normally this would be fine, except there is a fee to void a paper check that has already been shipped. Bill.com gives alerts when checks have not cleared after 30, 60, and 90 days. Then after 90 days they auto void the paper check and return the cash to the client's bank account.

Inability to mail a paper check without an email attached. A lot of vendors my client uses do not have an email address for bill pay. This has resulted in having to use my client's AP email for several vendors just to get a paper check mailed. Along with that comes the alerts to set up an account with QBO for all of the different vendors now associated with that account. Bill.com does have a network similar to QBO, and they will invite vendors to connect for digital payments IF the client has an email for the vendor AND wants to invite the vendor to connect. Not connecting does not impact the paper check writing process in any way.

Some clients use "positive pay" with their bank. Currently there is no way to download a list of checks mailed into CSV with check numbers that can be uploaded to their bank for auto approval.

Ability to see the printed check. One vendor this client sent a check to said that the name printed on the check was wrong. On our end the vendor looks correct, but without the ability to see the physical check that was printed, we cannot confirm.

The maximum amount that can be paid in 30 days. Like an ATM, QBO has a limit on the amount that can be withdrawn. The issue I have with this is that when the limit needs to be increased, it can take days for the approval to go through. Secondly, only the primary person can make that request. If you have a business owner that is not hands on with this process, explaining what you need them to do is a hassle. I also do not understand why QBO needs this feature since QBO pulls money from the client's account directly and then makes the payments. There is no risk to QBO since they are not using their money to make the payments. I understand that there might be back end legal stuff I do not know about for this one.

Bank account numbers & Chart of accounts. After getting the client set up with bill pay, and connected to the bank accounts, there was an issue with where the payment was recorded on the chart of accounts. In bill pay, you can choose what account to withdraw money from. Then later you have to choose what CoA to say the payment's came from. Even if the bank account is connected and already tied to a CoA. Example, Operating account 5555 and Savings account 2345 are connected in QBO and tied to CoA's "Operating" and "Savings". Then Operating account 5555 is set as the default account to pay bills from. Rather than automatically posting payments to the CoA "Operating" you have to choose where to record the payments on the CoA. If you are not careful, you can miss the second choice. This lead to several payments being listed on the QBO register as coming from the Savings account while the cash has physically come out of the Operating account.

Similarly, even if the accounts are set up/connected in QBO, the client still has to submit two months worth of bank statements before bill pay is approved. This can also only be done by the primary and not anyone else. Again, I am not sure if this bit is a legal issue, but it seems redundant since QBO already has the bank info. It is also a hassle to require only the primary to do the upload instead of their bookkeeper.

Credit memos - These are difficult to clearly assign/use, but they have gotten better since I started in September.

Reporting - It is difficult to run one report for what bills were included in the vendor payment. Most of the views will say "10 bills" make up X payment, rather than a list. this can make reconciliation a little more difficult for the vendor receiving the payment if there are a lot of revolving invoices.

Timing - It can take up to two weeks from processing the payment to when the check is written. Not shipped/delivered, written.

The inbox matching process needs work. Sometimes QBO recognizes that a bill in the inbox matches a bill already entered, but not often. This is more of a mild annoyance than a major hindrance.

Failed payments need more info as to why they failed. Then when the issue is corrected, the ability to permanently dismiss the failed payment error. I still have "5 failed payments" alert that pops up regularly even though I have corrected and processed them since then.