As a brief overview,  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. For general usage and first time connections, please see our article on Importing from QuickBooks Desktop.

❗ 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 first.

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 then we recommend stepping through the following troubleshooting steps in order before attempting to connect again.

1. Where is your file located?

It is often helpful to ensure that the file you are importing is on your local hard drive. This helps to isolate any networking or mapped network drive issues. 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 located in the same drive. This means that, if the Desktop Connector is on the C: drive, the .QBW file must also be on the C: drive. Ensure no other QuickBooks files are open, only the file for the company you are uploading.

To identify the exact location of the .QBW file you are uploading, have the file open in QuickBooks and use the 'F2' key or 'Ctrl + 1' keys to open the location information.

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 preferences are correct

Turn off 'Quick Startup'

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

Open your QuickBooks file and go to 'Edit > Preferences > General > My Preferences' and uncheck the 'Keep QuickBooks running for quick startups' option. 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.

Open your QuickBooks file and go to 'Edit > Preferences > Accounting > Company Preferences' and uncheck the 'Show lowest subaccount only' option. Save and close the preferences panel.

There is a small bug in the Intuit API that is triggered when this checkbox is enabled.

Allow applications to access the company file

Open your QuickBooks file and go to 'Edit > Preferences > Integrated Applications > Company Preferences' and uncheck the 'Don't allow any applications to access this company file' option. Save and close the preferences panel.

3. Reset the connection

You should check to see if there are any previous connections 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. Go to 'Edit' > 'Preferences' > 'Integrated Applications' > 'Company Preferences'.

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

Note that, after you connect successfully, you should see the application back in this list.

Other troubleshooting issues

Object reference not set to an instance of an object

If you see an error as pictured below it is likely 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 from

For more detail you can follow the conversation here:

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

There are two reasons this error can occur. First you should ensure that this option is disabled by following the instructions above in this article.

The other reason this can occur is if account codes are entered incorrectly.

If an account code is entered into the 'Name' field for an account then it can cause this 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.

Still having trouble?

If you are still running into problems and you have tried all of the above resolutions, please attempt the import or update again and then send us the support log to our support team at

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