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How to Reconnect Your QuickBooks File After Upgrading Webgility Desktop

This article helps Webgility Desktop users through the process of reconnecting QuickBooks Desktop into Webgility Desktop following an upgrade and offers solutions to common connection errors. Upgrading the Webgility Desktop application can disrupt the QuickBooks Desktop connection, especially when a new company file is involved.

Upgrading your Webgility Desktop application can disrupt your connection to QuickBooks if a new company file is introduced. Learn how to successfully reconnect QuickBooks to Webgility after an upgrade and fix common connection errors.

Causes of Issues

  • Old Application Certificate: The QuickBooks security certificate from Webgility is outdated or invalid.

  • Permission Conflicts: Webgility lacks admin rights or proper access in QuickBooks.

  • Wrong Company File: The incorrect QuickBooks file is open during reconnection.

  • Security Software Interference: Firewalls or antivirus programs may block communication.

  • Incomplete Upgrade: Webgility wasn’t properly updated or restarted post-upgrade.

Steps to Reconnect QuickBooks with Webgility

1. Upgrade Webgility Desktop

  • Download the Latest Version: 

    Navigate to Help > Check for Updates.
    Check the box labeled "Take Webgility database backup before proceeding with the update."
    Click Update.

    You’ll be prompted to choose a folder to save the Webgility database backup.
    Once the folder is selected, the application will proceed to update Webgility to the latest version.

2. Reconnect to the New QuickBooks File

  • Launch QuickBooks Desktop and open the Company file and login as Admin.

  • To confirm the QuickBooks Company File Name, press F2 or Ctrl + 1. In the Product Information window, you’ll see the Company File Location. Compare this location with the one shown in Webgility. If the locations match, Webgility should connect to QuickBooks successfully. If they do not match, copy the correct file path from QuickBooks and paste it into Webgility, then try reconnecting.

    Note: Make sure the Product Information window is closed before attempting to reconnect QuickBooks with Webgility.

  • Open Webgility Desktop.

  • Go to:
    Connections > Accounting/POS/ERP > Edit Connection > Test QuickBooks Connection 

    • Ensure QuickBooks is in single-user mode

3. Regenerate the QuickBooks Certificate

  • In QuickBooks:

    • Go to Edit > Preferences > Integrated Applications > Company Preferences.

    • If Unify Enterprise appears under “Applications,” select and Remove it.

    • Click OK to close Preferences.

  • In Webgility:

    • Attempt to reconnect QuickBooks.

  • In QuickBooks:

    • When the Application Certificate window appears, select:
      ✅ Yes, always; allow access even if QuickBooks is not running

    • If asked, choose the Admin user.

  • Finalize the setup.

    • Confirm Webgility is listed again under Integrated Applications.

4. Troubleshoot Common Connection Errors

  • Could not start QuickBooks:

    • Ensure both programs are running as Admin.

    • Verify the correct company file is open.

  • Certificate or Access Denied:

    • Remove any outdated certificates and regenerate the QuickBooks certificate.

  • General connectivity issues:

    • Temporarily disable firewalls or antivirus software.


Reference links

Quickbooks connection