Stripe to QuickBooks Desktop Install Guide

Before you begin, please ensure the option to "Automatically Apply Payments" is turned off in QuickBooks. This feature causes issues with payments being applied to the wrong invoices once the data is in QuickBooks.

  1. In QuickBooks, go to Edit then Preferences.
  2. Select Payment from the left menu.
  3. Click Company Preferences at the top.
  4. Uncheck Automatically apply payments.
  5. Click OK.

Helpful items to check before installing:

  • We recommend that you reboot (turn off and then back on) the computer that you are installing on, prior to installing.
  • You'll need to be logged into the computer that has QuickBooks and can access the company file, for the installation.
  • The preferred browsers we'd like you to install with are Chrome or Firefox.
  • The QuickBooks company file you wish to sync transfers to needs to be open during installation.
  • You need to be signed in as the Admin and in single user mode in Quickbooks for the install to work properly.
  • Occasionally an anti-virus and/or malware systems block the installation of our app. Disabling these only for the duration of the installation can help. 
  • We often see that if you right-click to "Run as Administrator" both QuickBooks and the Commerce Sync app, you'll see fewer issues during installation.

Installing Commerce Sync:


    1. Visit the Stripe Pricing page and select the monthly or annual plan then click the Start Free Trial button. 
    2. Sign-in to your Stripe account as the Administrator:


  2. Download and run the Commerce Sync installer
  3. Once the installer has finished downloading, open it and click Run                                                                      
  4. After you select Run, you should see the Commerce Sync for Desktop Screen "Starting Up"
  5. You will need to log into your Stripe account again at this point.
  6. Double check that you have QuickBooks open and the correct company file and click Continue
  7. In QuickBooks, you'll see a pop-up, check the box next to "Yes, always allow" then select “Continue.” Sometimes this screen is hidden behind other QuickBooks windows, if you don't see this screen minimize your other QuickBooks windows to find it. Note that when you are installing another location, this step is skipped.
  8. Select "Done" on the second pop-up.
  9. Select your settings for Commerce Sync: the time zone your Square account is in, whether you would like sales transferred into a Single Income Account or Sales by Category and what bank account for Commerce Sync to post the deposit information (what account Square is depositing to).
  10. Please enter your billing information. Your free 15-day trial starts today. After 15 days, your Commerce Sync subscription will begin.
  11. You'll see the Installation Complete screen and then click the View Dashboard button.
  12. At this time, we recommend opening the Commerce Sync for Desktop app up immediately and waiting for the sync to complete. The green arrows will stop spinning and the next sync timestamp will be showing. 
  13. Once the sync is complete, go to the Commerce Sync Web Dashboard and review your settings.



Going forward, each day Commerce Sync will transfer all of your sales information for the previous day to QuickBooks Desktop. This transfer will occur after midnight to ensure that all orders for the day are closed. Find out more information on transferring sales that you had prior to installing here.

Commerce Sync is now installed in your Square account and on your computer. You can access your Commerce Sync Dashboard and review your Settings in your Square account. Go to Apps, then My Apps and click the Launch button for Commerce Sync. To open the Commerce Sync app installed on your computer, open the shortcut from your desktop.

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