Square to QuickBooks Online Install Guide


Before you begin, please ensure the options for "Automatically apply credits" and "Automatically apply bill payments" are turned off in QuickBooks. These features cause issues with payments being applied to the wrong invoices once the data is in QuickBooks.

      Click the Gear icon at the upper right of your screen.

  1. Choose Account and settings.
  2. Select Advanced from the left menu.
  3. Click the Pencil icon for the Automation.
  4. Turn off the Automatically apply for credits.
  5. Hit Done.


  1. Sign-in to your Square account                                    
  2. Click on the Apps tab in your Square account (bottom left of the screen)
  3. Install the Commerce Sync app in your Square account:
    • For first time installations, click Get Started under the Commerce Sync app

      On the Permissions Screen, click Allow at the bottom
    • For multiple locations and return customers, click Manage Apps, Launch and then select your Location



During the next few steps you will be logging in to your QuickBooks Online account. This process takes place in the Commerce Sync Dashboard. If you need assistance with your sign-in information or account selection for your QuickBooks account, please reach out to Intuit Support by calling 800-450-8475.

  1. Click on the Connect to QuickBooks icon.

  2. Sign-in to your QuickBooks Online account using your QuickBooks Admin login.

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  3. If you have multiple QuickBooks company files, you will be prompted to select the one you'd like Commerce Sync to connect to.

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  4. After you have selected the QuickBooks company file, you will be asked to connect Commerce Sync to access your information. Click the Connect button so that Commerce Sync can transfer sales information to your QuickBooks account automatically on a daily basis.


  1. Commerce Sync will verify your connection to QuickBooks Online. Once you see the green check marks, select your bank account and click Continue.
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  2. Customize your Commerce Sync transfers: select the time zone your Square account is in and whether you would like sales transferred into a Single Income Account or Sales by Category. Then click Complete My Activation
  3. Please enter your billing information. Your free 15 day trial starts today. After 15 days, your Commerce Sync subscription will begin.
  4. Commerce Sync is now installed in your Square account and now connected to your QuickBooks Online account. On the Commerce Sync Dashboard click View under Settings to review your settings. This is how Commerce Sync will transfer your sales activity into QuickBooks



Going forward, each day Commerce Sync will transfer all of your sales activity for the previous day to QuickBooks Online. 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.

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