Showing results for 
Search instead for 
Did you mean: 
Level 3

Intuit Merchant Services Not Recording Deposits Correctly

There are errors with new way Intuit Merchant Services is automatically recording the deposits and fees. Now the deposit and fees are automatically recorded once all the payments have been added. The problem is that I have customers who pay with online bank checks and some who pay with credit cards. Intuit Merchant Center is creating separate deposits in Quickbooks for the bank checks and another one for the credit card payments however, they are depositing them together in one deposit to the bank. There are not two transactions for the fees, they are only recording one combined fee transaction in Quickbooks for both the checks and the credit card payments. Which leads me to believe they are indeed sending the deposit as one transaction to my bank, otherwise they would separate out the fees, one for each deposit.


I went through this over 3 years ago with them and they told me that it was my bank that was combing the deposits that they were not depositing them together. However, I do not believe this or there would be two fee transactions, one to match each deposit, not one fee transaction. I could work around it with the old way where we manually entered our deposits. I would just add the payments, go out of the Record Merchant Service Deposits screen, open Record Deposit and record all the bank checks and credit card payments together as one deposit instead of two the Merchant Center wanted me to do. 


Now that they are automatically adding the deposits and fees none of the deposits that have both cc and bank checks are matching up on our bank statement. Is there an option to bypass the automatic recording of the deposits and fees and be able to record them myself?

10 Comments 10
QuickBooks Team

Intuit Merchant Services Not Recording Deposits Correctly

Hi @azpcp,


It's nice to have you in the Community. I'd be glad to help share some information about recording merchant deposits.


The amount you received from the invoice will not match your bank statement because of the fees. You'll need to record the fees correctly so when you create a merchant service deposit on your QuickBooks Desktop (QBDT) it will match on your bank statement.


You can check out this article for more information and for the steps on how to manually record your deposits: Record Merchant Service Deposits.


Also, if you need help managing your deposit account information in the future, you can check out this helpful article: Manage your account information using the Merchant Service Center.


Leave a comment below if you have any other concerns. I'm here to help. Have a good day.

Level 3

Intuit Merchant Services Not Recording Deposits Correctly

@GraceC Per your answer, it's unclear if you understand how the deposits and fees are entered into Quickbooks from the Merchant Center.


The amount we receive from the invoice never matches the bank statement, but not because of the fees. Multiple invoices payments made on the same day are always batched together into one deposit. Fees are always a separate transaction and recorded separately from both the deposit and payment. There are three entries made into Quickbooks for each customer transaction made in the merchant service online payment network, a payment, a deposit, and a check for the fees.


The problem is that merchant services are sending one deposit to my bank, but are recording it as two deposits in Quickbooks when it includes both bank checks and cc payments.



Intuit Merchant Services Not Recording Deposits Correctly

Thank you so much for giving us more details, azpcp.


There's currently no option to separate a batch deposit to multiple bank transactions. However, there's an option to match the bank statement to multiple entries in QuickBooks Desktop. Let me show you how to use the Add More Details selection: 

  1. In the Bank Feeds Center,
  2. Select the Deposit and click Add More Details.
  3. Select the open invoices that need to be matched.
  4. Click on Add to QuickBooks. 1.PNG 2.PNG

Additional notes about this process is found in this article: Add and match Bank Feed transactions in QuickBooks Desktop


We are gathering customers' feedback about the services they are using. Yours must be sent so that our Product Developers will know there's a challenge when matching batch deposit to multiple entries in QuickBooks. 


It's our priority to make sure you get the help you need. If you have other questions, please post them here. 

Level 3

Intuit Merchant Services Not Recording Deposits Correctly



I don't want to separate them, I want them combined. Intuit is making one deposit into my bank account but entering them as two deposits in Quickbooks. All of our accounting is entered manually for various reasons that have nothing to do with this question so I won't go into it here, so we do not download our bank statements. We only use them to reconcile and the deposits are not matching up so we can reconcile.


Intuit Merchant Services Not Recording Deposits Correctly

Hey there, @azpcp.


When the system record the deposits in QuickBooks, the information downloaded will depend on the data shared by your bank. Since you've mentioned that Merchant Services is only sending one bulk deposit, I recommend contacting our QuickBooks Payments Team.


One of them will be able to take over and verify the payment deposited into your bank account. Another alternative would be to delete the unmatched transactions and receive payment manually on the invoice.


While receiving payments, make sure to select the Undeposited Funds account to deposit them all together. I’m attaching an article with detailed instructions on receiving the payment:


Deposit payments into the Undeposited Funds account in QuickBooks Desktop.


Aside from that, I'm also adding another article on how to delete the transactions entered from Merchant Services (scroll down to Delete unmatched transactions):


Add and match Bank Feed transactions in QuickBooks Desktop.


Reach out to me whenever you have additional questions or concerns. Please know the Community has your back, and I'm here ready to help you. Have a good one.

Level 3

Intuit Merchant Services Not Recording Deposits Correctly

This question received 3 different answers from 3 different people, all of which either did not understand how merchant services works and/or the question.


This question is in reference to these products specifically: *Desktop Pro 2019* & *Intuit Merchant Services* 


So I’m trying this again, with photos. 


There are errors with the way Intuit Merchant Services is automatically recording the deposits. The error only used to happen if with a combination of credit card payments and ACH payments. Now it is happening with multiple credit card payments. 


Merchant services will make a deposit into my bank account that combines credit card payments and ACH payments made on the same day. However, merchant services creates and records two deposit entries in QuickBooks, one for the credit card payments and the other for the ACH payments.  


For example, on 1/2/20 in the Record Merchant Service Deposits screen a deposit for $858.98 was recorded into my check register for credit card payments. (Picture 1) 

1_CC Deposit Automatically Recorded.png


On 1/2/20 a second deposit for $3147.00 was recoded into my checking register for Bank/ACH payments. (Picture 2) 

2_ACH Deposit Automatically Recorded.png


In the Transaction Reporting Screen/Intuit’s Merchant website it shows one deposit on 1/2/20 for $4005.98 which matched how the funds are deposited into my bank account. (Picture 3) 

3_Merchant Statement Deposit.png


The only way for me to fix this is to delete the two automatically entered deposits and re-record the deposit with both the credit card and ACH payments together. (Picture 4)



However, when I do this a Merchant Service Message pops up and says “The items you’ve selected for deposit will not match the single deposit on your bank statement. To better match this deposit with your bank statement, make sure this deposit: Does not include transactions that were processed with other card types.” (Picture 4)



I have to create this entry so that it will match my bank statement and Merchant Services is the one who is creating a deposit with multiple card types. They even have a statement on their website that says: “The check and card transactions are combined after 6/23/16.” (Picture 3-Center of image.) 

3_Merchant Statement Deposit.png


This only used to happen with a combination of credit card payments and ACH payments, now they are creating multiple deposit entries for even the same type of transaction. 


Two Visa payments were automatically recorded as two deposits in QuickBooks Check Register, the first for $186.85 (Picture 5&7) and the second for $360.00 (Picture 6&7), yet were actually deposited together as one deposit of $545.85 in my bank account. (Picture 8) 

5_First Deposit.png 6_Second Deposit.png 7_Check Register Two Deposits.png 8_Merchant Statement Deposit.png


The merchant center has now started automatically creating deposit entries once all payments have been added. Before the changes at the end of last year, I could at least just add the payments and create my own deposit entry and dismiss their multiple entries. Is there any way to get an option to bypass the automatic recording of the deposits and fees and be able to record them myself?



Intuit Merchant Services Not Recording Deposits Correctly

Hi, azpcp.


I appreciate the screenshots you've provided. QuickBooks only accepts the transactions provided by your bank. However, you have the option to unmatched the transactions and manually received the payments.


Ensure you select the Undeposited Funds when receiving them. You can refer to this article for the detailed steps and instruction: Deposit payments into the Undeposited Funds account in QuickBooks Desktop.


Also, you can check these resources to help you record the deposits from Merchant Services:


If you're still getting the problem, I'd suggest getting in touch with our Merchant Services Center. They have the tools required to perform any escalations in the system whenever necessary on your behalf.


You can contact them via this link:


Kindly update me on the results or if you need further assistance. I'll be around to provide additional help and insights whenever you need it. Have a great day!

Level 1

Intuit Merchant Services Not Recording Deposits Correctly

Give it up dude..  These people do NOT live in the real world.  They cannot see the issue.  I am having the same issue.  I called support and got nothing.  They tried to tell me that it was what I wanted.  No joy.  I am going to cancel merchant services if they don't fix these issues.  I use invoicing, and it's usually one CC or Check for each.  I batch at the end of the day, and that matches the bank.  No problem till Merchant Services.  Now nothing matches.  It is as though they are making things up, and my bank NEVER sees the deposits grouped like that so how can they be telling QB that information?  Just wondering...

Level 3

Intuit Merchant Services Not Recording Deposits Correctly

My advisor suggested I turn off the auto match & record option under the deposit settings to avoid this and have more control over how the deposits are recorded. I agree, it is not a banking issues.

Level 1

Intuit Merchant Services Not Recording Deposits Correctly

I wish that worked. I've NEVER turned on the Auto match & record feature and I've had this same problem intermittently for YEARS!!!  They convince me to upgrade to get support and the latest version to fix it and it STILL happens.  I use their help menu's and half of their links to more info don't even work so I'm stranded.  

The other problem with deleting them and re-entering the payment is all the extra time it takes to fix it, when THEIR faulty software should be fixed.  I've been using QB since 1999 and I'm starting to get fed up with all the crap.  3 different answers from 3 different reps and they still couldn't get it right.  Extremely sad for such a large company. =(

Sign in for the best experience
Ask questions, get answers, and join our large community of QuickBooks users.
Sign In / Sign Up

Need to get in touch?

Contact us