Before you begin, please ensure the Automatically Apply Payments setting is turned OFF in QuickBooks. This prevents payments from being applied to incorrect invoices after syncing.

Turn Off “Automatically Apply Payments” in QuickBooks

1. Open QuickBooks
2. Go to Edit → Preferences
3. Select Payments from the left menu
4. Click the Company Preferences tab
5. Uncheck Automatically apply payments
6. Click OK

Before You Install

Use the checklist below to help avoid installation issues.

Recommended Setup Checklist

✅ Reboot the computer before installing
✅ Install using Chrome or Firefox
✅ Open the QuickBooks company file you want to sync to
✅ Log into QuickBooks as the Admin user
✅ Switch QuickBooks to Single-user Mode
✅ Install on the same computer that hosts QuickBooks/company file access
✅ Temporarily disable antivirus or malware protection if installation is blocked
✅ Right-click and Run as Administrator for both:

• QuickBooks
• Commerce Sync for Desktop

Tip: If you experience Captcha issues, refer to the related troubleshooting article.

Step 1 — Connect Clover to Commerce Sync

1. Log in to Clover.com from the computer where QuickBooks is installed. Please Note: If you have more than one location be sure to have the correct one selected for the integration
2. From the left menu, click More Tools
3. Search for QuickBooks by Commerce Sync
4. Open the app listing
5. Click Connect
6. Select the Expert Plan (Required for QuickBooks Desktop users)
7. Click Accept

Step 2 — Connect Commerce Sync to QuickBooks Desktop

Download the Desktop Application

1. A new browser tab will open to the Activation screen
2. Select QuickBooks Desktop
3. The Commerce Sync for Desktop app will begin downloading
4. If prompted, click Run/Allow
5. Wait for the download to finish then proceed to the steps below

Connect Your Account

1. Open the newly downloaded CommerceSyncForDesktop_Setup
2. Click the Sign in to Commerce Sync button
3. A new tab will open. If you're still signed in click Open desktop app
4. Click back to the Commerce Sync application and go through the steps
5. One of the steps will ask for permission in QuickBooks. See below to Approve QuickBooks Access

Approve QuickBooks Access

Before continuing, confirm:

• QuickBooks is still open
• The correct company file is open in QuickBooks
• You are logged in as Admin
• QuickBooks is in Single-user Mode

When prompted for the permissions QuickBooks:

1. Select Yes, always allow
2. Click Continue
3. Click Done

Note:
If you do not see the Application Certificate window, it may be hidden behind QuickBooks. Minimize other windows and check again.

Additional Note:
When installing an additional Clover location, this authorization step may be skipped.

Step 3 — Customize Your Settings

1. Now that the app is connected, click View my Dashboard. This will open a new tab. If it doesn't take you directly to the dashboard you can go to clover.commercesync.com
2. Select one of the follow types of transfers:
   • Single Income Account
   • Sales by Category
   • Sales by Label (Revenue Class)
3. Click Complete Activation and it will take you to the main Dashboard
4. You can click the View button in the center under the settings box to view/change the mapping. Click SAVE at the bottom

Important: Wait for the First Sync

After completing the integration the application will run its first sync. This will populate the dashboard with the default accounts and items that you can change as needed with the above steps. We recommend letting the app finish its first sync to establish a connection with the company file

You’ll know syncing is complete when:

• The green sync arrows stop spinning
• A “Next Sync” timestamp appears

What Happens Next?

🎉 You’re Ready!

Commerce Sync will begin transferring your sales data to QuickBooks Desktop automatically.

Here’s what to expect:

• Sales from the previous day sync after midnight
• Transfers occur daily once orders are fully closed
• Historical sales can also be transferred if needed

Commerce Sync is now installed:

✅ In your Clover account
✅ On your computer

Accessing Commerce Sync Later

Open the Web Dashboard

1. Log in to Clover.com
2. Select QuickBooks by Commerce Sync from the left menu

Open the Desktop App

Use the Commerce Sync shortcut on your desktop.