This guide is provided by Conductor, the service that powers the QuickBooks Desktop integration for many business tools, including the one that sent you here.
Most QuickBooks Desktop users work in a single company file, the local file that holds all of a company’s accounting data. If you work with multiple company files on the same Windows computer, you can still sync each file with your QuickBooks Desktop integration. The key is that every company file gets its own Web Connector connection and QuickBooks Desktop must stay open with no file loaded. This guide explains exactly how to set that up, why the “blank” QuickBooks window is required, and what performance trade-offs to expect.

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1. Create a Web Connector connection for each company file

You will run your integration’s usual QuickBooks Desktop setup flow once per file.
1

Open the first company file in QuickBooks Desktop

Start QuickBooks Desktop and open the company file you would like to connect first. Sign in as the Admin user.
2

Run the QuickBooks Desktop setup flow for your integration

Follow the on-screen steps exactly as you would for a single-file installation. When you finish, a new row appears inside the QuickBooks Web Connector that is linked to only this company file.
3

Close the first file, open the next company file, and repeat

Close the first file, open the next company file, and rerun the setup flow. Keep repeating until every company file on the machine has its own connection.
When you are done the Web Connector will look similar to the screenshot below, one connection per company file:
QuickBooks Web Connector with multiple connections

The Web Connector after creating multiple separate connections – one per company file.

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2. ❗ Keep QuickBooks running without any company file loaded

QuickBooks Desktop must stay open with no company file whenever your integration needs to sync data. This lets the Web Connector open the correct file on-demand, complete the request, and then close it again.

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How to return QuickBooks to the No Company Open” state

  1. Open QuickBooks Desktop.
  2. Go to the “File” menu.
  3. Select “Close Company”.
QuickBooks Desktop without any company file loaded

QuickBooks Desktop showing the required "No Company Open" window.

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3. Best practices for a reliable multi-file setup

  • Use a dedicated Windows server: Most users managing multiple company files already have a Windows server in their office dedicated to managing their QuickBooks Desktop company files. Set up the Web Connector connections on this server and keep QuickBooks running there instead of on someone’s everyday workstation. That prevents a user from accidentally opening the wrong file and blocking syncs.
  • Launch QuickBooks Desktop automatically on startup. Add QuickBooks to the computer’s startup programs or create a Task Scheduler entry that opens it a minute after boot. This ensures QuickBooks Desktop is always open whenever the computer/server restarts, which eliminates the extra delay of QuickBooks Desktop having to launch every time you sync.

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4. Troubleshooting tips