Skip to content
  • There are no suggestions because the search field is empty.

Troubleshooting Guide for QuickBooks Online and QuickBooks Desktop Connection Issue with Webgility Online

This article helps Webgility Online users resolve connection issues between Webgility Online and both QuickBooks Online and QuickBooks Desktop. Users may face disruptions due to expired authentication tokens in QuickBooks Online or improper desktop extension setups with QuickBooks Desktop. The guide walks through reconnecting QuickBooks Online using OAuth, reinstalling and configuring the Webgility Desktop Extension, and confirming QuickBooks Desktop company file paths. It also includes advanced steps for resolving COM Class errors and finalizing the desktop integration to ensure smooth and uninterrupted data sync between systems.

1. Troubleshooting QuickBooks Online Connection Issues

Webgility Online connects to QuickBooks Online using secure OAuth credentials. If the authentication token expires or is revoked, you'll need to reauthorize the connection.

Steps to Reconnect QuickBooks Online:

1) Log in to Webgility Online and go to:
Settings > Connections

2) Verify the correct company file, navigate to: Settings > Accounting

Note: Take screenshots of your current configuration before reconnecting a new company file as this process auto resets the existing configuration. 


3) Disconnect the existing QuickBooks Online connection by clicking Remove

4) After disconnecting, click Add Accounting and select Connect to QuickBooks.
When prompted, grant access via the QuickBooks authorization popup and confirm the connection by clicking Connect.

2. Troubleshooting QuickBooks Desktop Connection Issues

The Webgility Desktop Extension facilitates communication with QuickBooks Desktop. If you’re encountering sync or connection errors, follow the steps below:

A) Reinstall the Webgility Desktop Extension

  • Use the latest installer provided in link

  • Reconnect and test the connection to QuickBooks after reinstallation.

B) Use Matching Login Credentials

  • Log into the Webgility Desktop Extension using the same credentials as your www.webgility.com login.

C) Confirm the QuickBooks Company File Path

  • Open QuickBooks in Single-User mode using an Admin account.

  • Press F2 and copy the path listed under "File Information".

  • In the system tray, right-click the Webgility Desktop Extension > Remove old file path > Paste the new one.

  • Click Connect to QuickBooks. If successful, you’ll see a “Successfully connected to QuickBooks” message.

If you encounter a “COM Class” error during this step, continue with the following fix.

3. Connect Webgility Desktop Extension to QuickBooks Desktop

A) Close all Webgility Desktop Extensions and QuickBooks Desktop applications.

  • Navigate to: C:\Webgility\UnifyExtension

  • Right-click UnifyMergeModule.msi and select Install.

B) Launch the Webgility Desktop Extension and open the connection window.

  • Click Connect to QuickBooks.

C) When QuickBooks prompts with an Application Certificate:

  • Select “Yes, always allow access even if QuickBooks is not running”.

  • Under “Login as”, select Admin.

  • Confirm by clicking Yes.

D) Finalize the connection:

  • Click Continue > Done in QuickBooks.

  • In Webgility, click OK, then Save & Close.