Troubleshooting QuickBooks Desktop
Steps to follow if you are receiving an error message when importing or updating from QuickBooks Desktop
Daniel Walls avatar
Written by Daniel Walls
Updated over a week ago

❗ Note: This article provides a series of troubleshooting steps designed to help if you are unable to connect to the the QuickBooks company file. If you are having any trouble downloading or starting the Fathom Desktop Connector please read our article on troubleshooting the desktop connector.


Troubleshooting the Connection between Fathom and QuickBooks Desktop

The QuickBooks Desktop application allows third party applications to connect and extract financial data. To import or update company data from QuickBooks Desktop you can use the Fathom Desktop Connector.

💡Pro Tip: For general usage and first time connections, please see our article on Importing from QuickBooks Desktop.

When you add a file using the Fathom Desktop Connector and locate it on your computer, you need to have the exact same file open in QuickBooks at the same time for the initial connection to succeed.

If you are having trouble connecting to QuickBooks, then we recommend the following troubleshooting steps:

1. Ensure you are opening the .QBW file in the Desktop Connector with the same pathway used in QuickBooks

This helps to isolate any networking or mapped network drive issues. 

❗ Note: If you are using QuickBooks Desktop in a remote server environment, please see our 'Using the Fathom Desktop Connector in a Server Environment' article.

The Fathom Desktop Connector and the QuickBooks file (.QBW file) you are uploading into Fathom must be opened using the same file pathway.

For example: The company file opened in QuickBooks has the following location (C:\UserX\YourUsername\My Documents\.QBW file name). After selecting 'Add files' in the Desktop Connector, the file explorer would open. In this case, in the file explorer, you would select:

  1. The 'C:' drive in the left side column

  2. The 'UserX' folder

  3. The 'YourUsername' folder

  4. The 'My Documents' folder

  5. Finally, the '.QBW file name' QuickBooks file

The file pathway is determined by the location of the QuickBooks company file. To identify the exact location of the .QBW file you are uploading:

  1. Have the file open in QuickBooks

  2. Use the 'F2' key or 'Ctrl + 1' keys on your keyboard to open the location information

  3. The file location is the file pathway you must follow when selecting 'Add files' in the Desktop Connector.

❗ Note: It’s important to note the type of file being selected. While rare, sometimes a user will attempt to load a backup version of the file ('.QBB') rather than the actual file with the '.QBW' extension.

2. Ensure no other QuickBooks files are open

To make sure no other QuickBooks files are open, you should open the Windows Task Manager.

  1. Open the Task Manager by selecting ‘Ctrl’, ‘Alt’, and ‘Delete’ on your keyboard. Or search for ‘Task Manager’ in the Windows start menu.

  2. Go to where QuickBooks Desktop is listed in the Task Manager

  3. If you have more than one company open, close any and all company files except the company you are attempting to upload.

  4. If you have multiple files of the same company open, close all but one of the company files to ensure there are no duplicate files open.

3. Ensure preferences are correct

Turn off 'Quick Startup'

This preference is known to cause problems for third party applications trying to connect.

  1. Open your QuickBooks file

  2. At the top, select 'Edit'

  3. Go to 'Preferences'

  4. In the preferences panel, select 'General'

  5. Then, select 'My Preferences'

  6. Uncheck the 'Keep QuickBooks running for quick startups' option.

  7. Save and close the preferences panel.

Disable 'Show lowest subaccount only' when importing from QuickBooks Enterprise

When you attempt an import from QuickBooks Enterprise you may be required to configure your preferences in QuickBooks first. There is a small bug in the Intuit API that is triggered when the show lowest subaccount only preference is on. To turn this preference off:

  1. Open your QuickBooks file

  2. At the top, select 'Edit'

  3. Go to 'Preferences'

  4. In the preferences panel, select 'Accounting'

  5. Then, select 'Company Preferences'

  6. Uncheck the 'Show lowest subaccount only' option.

  7. Save and close the preferences panel.

    💡Pro Tip: If you are receiving an error message stating "Unable to import data when the 'Show lowest subaccount only' preference is active" and this option is not checked, then it may be an account naming issue. You can resolve this by following these instructions.

Allow applications to access the company file

  1. Open your QuickBooks file

  2. At the top, select 'Edit'

  3. Go to 'Preferences'

  4. In the preferences panel, select 'Integrated Applications'

  5. Then, select 'Company Preferences'

  6. Uncheck the 'Don't allow applications to access this company file' option.

  7. Save and close the preferences panel.

4. Reset the connection

You should check to see if there are any previous connections between QuickBooks and the Fathom Desktop Connector and, if so, remove them so we can create a fresh link. This should be done in all scenarios but is particularly pertinent if you see an error message like this:

"This application does not have permission to access this QuickBooks company data file. The QuickBooks administrator can grant access permission through the Integrated Application preferences."

To remove any existing connections:

  1. Log into QuickBooks company file in single user mode as the company administrator.

  2. At the top, go to 'Edit'

  3. Select 'Preferences'

  4. In the preferences panel, select 'Integrated Applications'

  5. Choose 'Company Preferences'.

  6. Select and remove 'Fathom Connector' from the list if it is there.

When you attempt to upload the company file with the Desktop Connector, you'll notice that the QuickBooks icon will start to flash orange after you 'Add Files' and select the QuickBooks company file.

Click on the QuickBooks icon and you should see window allowing you to grant permissions for the Desktop Connector to read the QuickBooks file. This will allow the Desktop Connector to connect to the QuickBooks file for a successful upload.

The Fathom Desktop Connector will once again appear on the Integrated Applications list in QuickBooks, as expected.

5. Attempt the upload again

Follow the steps to import the QuickBooks Desktop file into Fathom with the Fathom Desktop Connector.

If the import remains unsuccessful, you may be encountering one of the additional troubleshooting issues listed below.

Other troubleshooting issues

You may receive more specific error messages when attempting to import to Fathom from QuickBooks Desktop, including:

QuickBooks administrator must grant permission to access the file

If you reset the connection and still receive an error message stating that the Connector does not have permission to access the QuickBooks file, then you may be running QuickBooks as an administrator.

The Fathom Desktop Connector and QuickBooks need to be run at the same permissions level. This means, either both the Connector and QuickBooks need to be run as an administrator or both need to be run as a non-administrator in Windows.

To resolve this issue, run the Fathom Desktop Connector as an administrator using the following steps:

  1. Close the Fathom Desktop Connector, if it is open

  2. Locate the Fathom Desktop Connector using the 'File Explorer' in Windows. If you downloaded the Connector recently, it will likely be in your 'Downloads' folder.

  3. Right-click on the Fathom Desktop Connector

  4. Select 'Run as administrator'

  5. Look out for a permissions pop-up appearing in QuickBooks after you select 'Add files' in the Connector. This will allow you to grant the Fathom Connector access to the QuickBooks file.

Object reference not set to an instance of an object

If you see an error as pictured below it may be due to a bug introduced in QuickBooks Desktop 2019 R3. This bug affected multiple third party applications and once installed affects all versions of QuickBooks Desktop on the same machine.

This has been resolved by Intuit and the quick solution is to download and install 2019 R5 or later.

If you are on a version of QuickBooks Desktop newer than 2019, then please access the Support Log and QuickBooks SDK log and send a copy of both logs to our support team via the support messenger or via email at This will help us determine why you might be receiving this error.

Unable to import data when the 'Show lowest subaccount only' preference is active.

First you should ensure that this option is disabled by following the instructions above in this article.

If that option is unchecked and you're still receiving this error message, then the account codes may be entered incorrectly in QuickBooks. If an account code is entered into the 'Name' field for an account then it can cause this error message to appear.

For example: We sometimes see accounts where the 'Name' is set to '1000 · Rental Expenses' and the 'Code' is left blank. Rather, the name field should be 'Rental Expenses' and the code field set to '1000'.

To resolve this, go to the account settings in QuickBooks Desktop, to the specific account and update the name and code.

It is possible that other accounts are in the same state. You can view the Support Log after attempting an import to see which account is causing the issue. It may be faster to go through all the accounts and ensure that the code is entered correctly.

Did this not resolve the issue?

Feel free to contact our support team using the support message option or via email at If possible, please provide us with a copy of both the Support Log and QuickBooks SDK log when you reach out and a screenshot of any error message you might be receiving.

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