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oldtimer
New Member
October 25, 2024
Question

Merchant Services deposits entered twice in Enterprise

  • October 25, 2024
  • 15 replies
  • 87 views

I'm using Enterprise. This month there have been 2 payments (from 2 separate clients) that have been entered twice in my register.  However, only one payment shows up in each client's file.  I can only delete them out of the register (I can't find them anywhere else), and each time I go into Merchant Services, the duplicates get entered into the register again.

15 replies

K
Kurt_MQuickBooks Team
QuickBooks Team
October 25, 2024

We appreciate you reaching out here in the Community space. We'll help you resolve duplicate deposits inside QuickBooks Desktop (QBDT), @oldtimer.

 

Please be aware that if you're using both QuickBooks Bank Feeds and Merchant Service Deposits, this action will duplicate the information inside the program. Thus, you'll want to select which method to use to avoid having duplicate transactions in your company file.

 

Once you're ready to select which method to use when bringing in payments, you can utilize the Dismiss feature or manually delete the duplicate payment. We'll outline the steps to get you going:

 

  1. Access your QuickBooks Desktop company.
  2. From the Banking▼ drop-down menu, select Record Merchant Service Deposits.
  3. In the Add Online Payments tab, select the payments you want to delete.
  4. Select Dismiss Selected Payments.
  5. When a warning message appears, select OK.
  6. In the Ready to record window, deposits show the dismissed transactions prior to recording.
  7. Once recorded, it would show the amount of the deposit, minus the dismissed transactions.

 

Feel free to check this page for more information: Duplicate entries when downloading merchant service deposits into QuickBooks.

 

In case you only use Bank Feeds or Merchant Service Deposits, and the issue persists, we recommend reaching out to our Customer Care Team so they can conduct a further investigation: Contact Payments Support.

 

We encourage you to explore these articles to help resolve QuickBooks Payments issues and monitor your sales and expenses through customers, jobs, and reports:

 

 

We're always here to offer support if you need help with customer payments or have further inquiries regarding QuickBooks. Feel free to visit us or leave a comment below, and we will be glad to assist you. Stay safe

O
oldtimerAuthor
New Member
October 25, 2024

The option you suggest under Banking is not offered to me (Desktop v Enterprise, perhaps?).  I've been over the other page you suggest as well.  I am not doing the Bank Feeds through QBs.

 

It is maybe a connectivity issue - although I've had those for a long time (experiencing QBs having to shut down often when I click on Merchant Service Deposits).   I'll try Payments Support.

D
dc2025
January 15, 2025

Hello - I've had this same exact problem. I'm curious if you ever found a solution?

S
shislop
New Member
August 5, 2026

Have also had this multiple times and now I have a large ghost-balance in a reconciliation expense account on my P&L. There is no option to dismiss these transactions and if deleted, they redownload and post to the cash account. 

K
KenoLee_PQuickBooks Team
QuickBooks Team
August 5, 2026

When payments are processed through Merchant Services, QuickBooks Enterprise automatically downloads them; manually entering them and then deleting duplicates leaves background files active, creating a "ghost balance." Instead of deleting, you must match them.

 

Here is how to fix this:

 

  1. Go to the Banking menu at the top.
  2. Select Record Merchant Service Deposits.
  3. Locate the transactions and select Match to link them to your manual register entries instead of creating new ones.

 

To prevent future discrepancies, review the official Intuit guide on managing duplicate Merchant Service Deposit downloads.

 

Since the previous deletions caused incorrect balances, use a Journal Entry to fix your P&L:

 

  1. Go to the Company menu at the top and select Make General Journal Entries.
  2. Set the entry date to the end of the affected period.
  3. Line 1: Select your reconciliation expense account and enter the total ghost balance amount under Credit.
  4. Line 2: Select your cash/bank account and enter the same amount under Debit.
  5. Click Save & Close.

 

Please consult with your accountant before posting journal entries to ensure absolute accuracy for your specific books.

 

Moving forward, let the Merchant Services window guide your recording rather than entering payments manually first.

 

For a complete breakdown of the automated matching workflow, you can review the Intuit Guide to Automatically Recording QuickBooks Payments Bank Deposits.

 

Feel free to chime back if you need more help.

 

S
shislop
New Member
August 5, 2026

When I open the Banking menu and then Make Merchant Service Deposits, what is displayed is the Pending for Deposit list of payments received, but there is no “match” option. The only options that I have are to click Add Payment, or to close the window. There is no checkbox to select the transaction, there is no Dismiss button displayed. 

S
shislop
New Member
August 5, 2026

@oldtimer were you able to find  a solution or reason for this problem?

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