There are two main causes for duplicate entries when downloading QuickBooks Merchant Service Deposits:

  • You are already using QuickBooks Online Banking to reconcile bank deposits (thus downloading the same information as the Merchant Service Deposits process). This is the most common cause for duplicate deposit entries.
  • Connectivity issues when communicating with our systems.

Bank account or transaction in QuickBooks is changed or adjusted in some way

The Record Merchant Deposits and Fees windows looks at the QuickBooks account specified.

Other causes and solutions



1. Since using both processes duplicates the information in QuickBooks, you will need to determine which solution best fits your business: QuickBooks Bank Feeds -or- Download Merchant Service Deposits


IMPORTANT: Using the QuickBooks Bank Feeds process may be a better choice for reconciliation in QuickBooks as it downloads all your banking information versus the Merchant Service Deposits utility which only downloads deposits as they relate to your merchant service transactions. Remember, you can download the Merchant Service Fees separately if you decide to use the QuickBooks Bank Feeds option.


2. Connectivity issues may have various causes:


  • Corrupted QuickBooks add-on files.
  • Damaged QuickBooks data file (In QuickBooks go to  File►Utilities►Verify Data.  If there is any data problem contact QuickBooks Software Support (888-320-7276) to resolve. 
  • Improper system configuration for merchant services (Merchant Services does not support Terminal services, VPN, Remote Access, Windows Emulation or other non-native PC environments).
  • Bank account information changed during download time period - if the bank account has been changed, be sure to set the date for downloading to the day after the change occurred to properly capture those transactions.