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Troubleshooting guide for QuickBooks Online and QuickBooks Desktop connection issue with Webgility Online
Troubleshooting guide for QuickBooks Online and QuickBooks Desktop connection issue with Webgility Online

Troubleshooting guide for QuickBooks Online and QuickBooks Desktop connection issue with Webgility Online

David Pond avatar
Written by David Pond
Updated over a week ago

Troubleshooting guide for QuickBooks Online and QuickBooks Desktop connection issue with Webgility Online

Webgility and QuickBooks need to be connected properly to ensure seamless data exchange between them. However, sometimes the connection between QuickBooks and Webgility breaks and needs to be reconnected.

Webgility Online integrates with QuickBooks Desktop (Pro/Premier/Enterprise) and QuickBooks Online.

In this article, we will guide you through the troubleshooting steps for QuickBooks connection issues.

Connection issues with QuickBooks online

QuickBooks online integration breaks with Webgility online in case of authentication certificate expiration or due to any other authentication-related changes in QB.

However, it's effortless to reconnect QuickBooks online, no matter what was the reason for the connection break. Just follow the steps below:

1). Login to Webgility online and go to Settings> Connection.

2). We need to disconnect QuickBooks and connect it again.

(While reconnecting to QuickBooks online make sure that you are reconnecting to the same company file, else the current settings in Webgility will be set to default if you connect to a different company file if you are not sure then you can take screenshots of settings under Settings> Accounting)

Select ‘Yes’ for confirmation.

Once QuickBooks is disconnected, click on the 'Add Accounting’ button.

Click on ‘Connect to QuickBooks

You will get a permission popup, click on ‘Connect’

The data will start downloading

Click on ‘Let's Go’ button

Once you are reconnected with QuickBooks then go to Settings> Accounting, verify and Save all settings again, and then try to process orders.

Connection issues with QuickBooks Desktop.

In order to fix connection issues between the Webgility Extension and QuickBooks desktop follow the below steps:

Step 1: Re-install the extension using the below article and then test QuickBooks connection. (

(While logging into the extension make sure that you use same credentials that you use to login on

For testing QuickBooks connection follow the below steps:

1). Login to QuickBooks in a Single-User mode with admin credentials.

2). Press F2 button, copy the company file location and close the popup.

3). Right-click on the Webgility Extension icon from the system tray, remove the old location, paste the new one, and click on ‘Connect to QuickBooks’.

Click on the ‘Connect to QuickBooks’ button.

You will get the ‘Successfully connected to QuickBooks’ popup.

Click on ‘Save & Close

If you are getting an error while testing the connection then skip to other steps.

Once connected click on ‘Manual sync now

Step 2: Install the Webgility merge module.

If you are getting a “COM Class” error while connecting QuickBooks then follow this step if not please skip to the next step.

1). Go to C drive> Webgility> UnifyExtension, locate ‘Unify MergeModule’, do a right-click, and select Install.

After installing Merge Module, if you still get the “COM class” error then turn on the .NET features by following the below steps and installing the Merge Module again.

For enabling .NET framework please follow the steps below:

1). Find “Turn windows Features on or off” option in windows search and open it.

2. Enable the highlighted features and click OK

Select ‘Let Windows update download the files for you’

Once the download process is complete, install the Module again and try the connection.

Step 3: Regenerate QuickBooks certificate.

If the connection is still not working then please follow the below process to regenerate the QuickBooks certificate:

1. Open QuickBooks and login a single user mode with admin credentials.

2. Go to Edit> Preferences.

3. Under Integrated Applications go to Company Preferences and remove ‘Unify Extension’ certificate from the list and click OK

4. Open the connection window in Webgility Extension and click on ‘Connect to Quicbooks

5. You will get a Connection Certificate popup in QuickBooks, Select ‘Yes always allow access even if QuickBooks is not running’ and under ‘Login as’ select ‘Admin’. Click on Yes for the confirmation popup.

Click on Continue and Done

6. Now in the Webgility Extension you will get a Successfully connected popup, click on Ok and Save & Close.

After trying the above solutions, if you still face QuickBooks connection issues, please feel free to contact Webgility support at

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