Hello there, Hull Girl.

When you receive this message alert, it means that there's a problem that you need to fix. No worries, I'll help and make sure you handle this properly.

First, let's determine which payments were in the deposit. Log in to your Merchant Service Center. Once you get in there, select Payments, then Manage Account. In the Activity & Reports section, select Deposits. You'll then have to choose your recent deposit to see the individual payments.

Once done, record the deposit in QuickBooks. Make sure the amount is the same as what you have in your payments account. Here's how:

1. Go to the +New button.
2. Select Bank Deposit under Others.
3. Choose the QuickBooks Payments section.
4. Match the payments in the list to the payments in the Merchant Service Center report.
5. Click Save and close.

If the reconciliation needs to correct, you can manually unreconcile and reconcile them again. You can refer to this article for details: 

Reconcile an account in QuickBooks Online. 

Also, you can check this article to learn on how to prevent this issue from happening again: Make sure QuickBooks knows which account to record deposits to. 

Please let me know if you have other questions. I'll be around to help you more. Take care always.

Thanks for your reply. I am trying to do what you recommended. I recorded the deposit, but remember the deposit was already reconciled and matched. So now the deposit is in there twice. Once, when QB automatically completed the transaction, and again when I just did it. Deleting either of the transactions just puts me back where I started.  Advice? Thanks!

Hello, thank you for your reply. I am trying to do your recommendations...when I record the deposit, I now have 2 deposits for the same amount. When I try to delete one of them, I end up in the same place I started. In other words, these payments that QB says weren't automatically recorded are already there. What am I doing wrong? Thanks so much.

Good morning, @Hull Girl. 

Thank you for the extra clarification on the issue with payment deposits. I can get you in the right direction to get this resolved as soon as possible. 

Since you've tried the steps my colleague provided and it would put you back in the same position as before, I recommend contacting our Customer Support Team. They'll be able to use a screen share to get a better understanding of what's going on and then escalate the problem if need be. Here's how: 

1. Go to the Help icon in the top right-hand corner. 
2. Click the Contact Us button. 
3. Give a brief description of the problem and hit Let's Talk. 
4. Scroll down and choose to Get a callback. 

Afterward, you'll receive an estimated time of when they will get in touch with you. 

I hope these details help. If you have any other concerns, feel free to ask. I'm only a post away if you need me. Take care! 

Did you get this resolved? I'm having the same issue.

Thanks for joining us in this thread, marcfuller.

Have you already tried the steps given in the original response? It discusses how to determine what transaction the error message is referring to and how to resolve the issue as well. 

Please take note that in order for QuickBooks to automatically record deposits, there needs to be a matching sales receipt or payment received on an invoice.  For example, if you process a payment in the Merchant Service Center there won’t be a matching sales receipt in QuickBooks and the automatic deposit will fail. This is why it's important to process all your payments using QuickBooks online.

Just in case you're unable to record the deposit manually, I'd recommend reaching out to our QuickBooks Merchants Support Team. Here's how to reach out to them: 

1. Click the Help menu in the upper-right hand corner of your QBO account.
2. Type in "Talk to a human" in the chatbox, then press Enter.
3. Select Get help from a human.
4. Click Chat with us or Have us call you. 

You can also follow these steps to prevent this issue from happening again:

1. Go to the Gear icon ⚙, select Account and Settings, and then click Payments.
2. In the Chart of Accounts section, select the bank and expense accounts QuickBooks should use.

Additional guidance and future reference can also be found here:

• Record Payments Deposits and Fees in QuickBooks Online
• Common Questions About Payments Deposits in QuickBooks Online

You can always count on us and post questions in the Community if you need help again. We're always here to guide and assist you.​​​​​​​

I have also been having this issue for several months.  QB will auto match credit card payments to the transactions and then automatically create a deposit.  It is auto-matching e-check payments to transactions, but doesn't create the deposit.  They sit in Make Deposits until I manually create the deposit.

This creates two separate deposits in QB, which don't match to actual bank transactions.  I'm on with support now trying to get a better answer.  I'm extremely dissatisfied with the payments solution at this point.  The fees are higher and it's creating more work.

Having the same problem.... was super hopeful this thread would have a fix. Did you figure out an answer?

p.s. i hereby solemnly swear to bookmark this page and post an answer once i figure it out!

We understand the importance of having QuickBooks Payments to record the deposits automatically, @sscotney. I'm here to assist you in resolving this issue so you can continue doing business with us.

QuickBooks automatically adds the deposit if there's a matching sales receipt or payment on an invoice. If it doesn't, you'll get an alert that some QuickBooks Payments deposits weren't automatically recorded. After you receive the funds in your account, record them manually as a Bank Deposit.

First, we'll need to find out which payments are in the deposits by following these steps:

1. Go to Settings, then select Account and settings.
2. Click Payments, then Manage Account.
3. Choose Activity & Reports, then Deposits.
4. To view the separate payments, select the most recent deposit.

To match your total deposits, you'll need to record all the missing transactions in QuickBooks Online by following these steps:

1. Click + New, then select Bank Deposit.
2. Choose the QuickBooks Payments section.
3. Match the payments listed with those in the Merchant Service Center report.
4. Click Save, then Close.

If the issue persists, I recommend contacting our QuickBooks support team for further assistance in identifying and resolving the root cause.

Furthermore, to prevent this from happening in the future, ensure that your deposits go to the right accounts.

If you have additional concerns about QuickBooks Payments deposits, please don't hesitate to reply below. We're always here to assist you.