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How to Sync Transactions with QuickBooks® Desktop

Note: QuickBooks Desktop Sync is only available with selected plans.


The sync feature only works with QuickBooks Desktop. It does not work with QuickBooks Online. Please contact your customer success manager if you are interested in connecting your PEX account with QuickBooks Online.

QuickBooks Desktop Sync

QuickBooks Desktop Sync currently supports syncing with the U.S. editions of:

  1. QuickBooks Financial
  2. QuickBooks Enterprise Solutions (2015 or later)
  3. QuickBooks Premier (2015 or later)
  4. QuickBooks Pro (2015 or later)

How to Sync Transactions with Quickbooks Desktop

QuickBooks Desktop Sync has three main steps:

  1. Configuring the Connection (in most cases this is a one time setup)
  2. Setting up the Web Connector
  3. Syncing the Transactions

1. Configuring the Connection

Choosing a Bank Account

In QuickBooks Desktop, the chart of accounts is defined in company file. You need to have a bank account against which all PEX transactions will be recorded.

Enter that bank account manually in the “Bank Account” field. The name entered in PEX configuration should match exactly the bank account name they have created in QuickBooks Desktop.


Enter Bank Account Information

Mapping Your PEX Tags (optional)

Customers on the PRO or Infinite Plans have the option to manage transactions using the PEX Tag manager.

You can map up to two tags from PEX to QuickBooks Desktop:

  1. Expense Account: This is the main classification tag for an expense. You can choose a PEX tag from the drop down list to map to Expense Account tag. The value of this tag will be used to populate the Expense Account field in QuickBooks Desktop.
  2. The Default Expense Account: This is the default value used to populate the Expense Account in QuickBooks Desktop, if no PEX tag was assigned to the transaction.
  3. Expense Class: This is the secondary classification. You can select a PEX tag to map to Expense Class in QuickBooks Desktop. 

If your organization is not using the PEX tag manager, you will only have the option to choose a default Expense Account. No drop down list will be provided in that case.

Please make sure your PEX tags are properly set up in PEX tag manager. "Option Value" for a tag should match exactly with the account name (with out the numeric part) from your Quickbooks company file. For example,

Account Name in Quickbooks "Option Value" in PEX tag manager
    5420.Vehicle Expense     Vehicle Expense


Setting a Date Range (optional)

The default option is to sync “All available transactions” 

  1. This includes all transactions from the date you last synced, until the present date
  2. If you are running sync for the first time, then this option will sync all transactions in the last 12 months

To test connectivity, or to sync only a limited number of transactions, you should choose the second option, to sync “All transactions in a date range”

  1. If you choose "All transactions in a date range,” then you must specify a Start date
  2. Choosing an End date is optional
    • If an End date is not specified, the current date is considered to be the End date

Note that the date of transaction settlement is used when evaluating the Start and End dates.

  1. All transactions settled between the Start date and End date will be synced

If you are using the "Auto-Run" setting for WebConnector (see step 2 below), do not specify an End date.


Setting the Date Range

Transaction Approval Status

You can also choose to sync transactions based only on their review approval status.

The options are:

  1. To sync all transactions regardless of status
  2. To sync only approved transactions
  3. To sync both approved transactions and ignored transactions
    • The last option -- to sync approved transactions and ignored transactions -- will not sync any transactions that were rejected


Select Transactions by Approval Status

2. Web Connector Setup (one time set up only)

We integrate with QuickBooks Desktop via the Intuit Web Connector. You need to have the Web Connector application installed in order to use this feature. It is usually installed with QuickBooks Desktop.

You can also download the QuickBooks Web Connector if you don't already have it.

  1. Open the Intuit Web Connector
  2. If prompted, grant the Web Connector permission to access QuickBooks
  3. Click on “Add an Application”
  4. Select the Web Connector file downloaded in the previous step
  5. Click “OK”
  6. Select the last option “Yes always: allow access even if QuickBooks is not running”
  7. Click “Continue”
  8. Input your PEX admin password in the Password column
  9. If you want to perform a one-time sync, uncheck the “Auto-Run” check box
  10. Select the check box on the leftmost column
  11. Click the “Update selected” button


QuickBooks Web Connector -- Set to Auto-run Every 2 Minutes

3. Transaction Sync

You can choose to run the transaction sync once (manual sync), or you can set it to auto-run every selected number of minutes. 

Auto-Run Sync

  1. Check the “Auto-Run” check box
  2. Set the time interval in “Every_Min” column.

Transactions will be synced automatically after every X minutes, as you specify.

Manual Sync

  1. Uncheck the “Auto-Run” check box
  2. Each time you want to sync transactions, click the “Update Selected” button


Things to Keep in mind

  1. QuickBooks Desktop Sync does not allow one to use the transaction review in the QuickBooks Bank Feed. It will post transactions directly to the company file.
    • To review transactions prior to posting into QuickBooks, use the PEX transaction review process
  2. For the first time sync, it is always advisable to use the date range option.
    • Make sure all transactions appear as expected before selecting "All available transactions”
  3. Once the Sync process has started, it cannot be stopped or cancelled
  4. The process will sync all transactions that affect the customer’s PEX account balance, including:
    • All PEX card transactions (network transactions)
    • All fees (e.g., monthly account maintenance fee, any shipping fees, ISA fees)
    • All ACH debits and credits
    • Wire transfers
    • Merchant credits
  5. Please make sure you have a "Vendor" in Quickbooks company file for each Merchant of your PEX card's transactions. Alternatively, a "Default Payee" can be configured.  



* Screenshots of the QuickBooks Web Connector are reprinted with permission © Intuit Inc. All rights reserved.

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