Clover 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.

Click on the - and + symbols to expand and collapse sections.

  • 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.
  • If you have issues with Captcha, check out this article.
  1. Log in to from a browser on the computer where you have QuickBooks installed.
  2. From the menu, click More Tools
  3. Look for or type in "QuickBooks by Commerce Sync" in the search bar at the top right.
  4. Click on the QuickBooks by Commerce Sync app.
  5. Click Connect
  6. Select the Expert plan (this plan is required for QuickBooks Desktop users) and then click Accept.
  1. A new tab will open to the Activation screen prompting you to select your accounting solution.
  2. Click the QuickBooks Desktop icon to start the installation.
  3. The Commerce Sync for Desktop application will start to download if prompted click Run.
  4. Next, you should see the Commerce Sync for Desktop Screen "Starting Up"
  5. Click Connect, located towards the top right
  6. Once again, select the Expert plan and then click Log in to connect
  7. You will need to log into your Clover account again and then Open App
    1. If you have multiple Clover locations, select the correct location/store
    2. Select the Commerce Sync app on your Home Page at this point.
  8. Double-check that you have QuickBooks open and have selected the correct company file. Remember you must be logged in as Admin and in single-user mode.
  9. Click
  10. In QuickBooks, you'll see an Application Certificate pop-up, select Yes, always allow then select Continue and Done. 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.
  1. Select whether you would like sales transferred into a Single Income Account or Sales by Category.
  2. Click Complete My Activation.
  3. You'll see the Installation Complete screen and then click the View Dashboard button.
  4. 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.
  5. Once the sync is complete, go to the Commerce Sync Web Dashboard and review your settings.
YOU'RE READY! YOU'LL SEE YOUR FIRST SYNC TOMORROW! 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 Clover account and on your computer. You can access your Commerce Sync Dashboard and review your Settings in your Clover account. Log into your Dashboard and click on the QuickBooks for Commerce Sync option in your left menu. To open the Commerce Sync app installed on your computer, open the shortcut from your desktop. 
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