Authorize.Net 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 transfer 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.

Install Commerce Sync on Authorize.Net:

  1. Click here to begin activation. You will be need to log in to Authorize.Net as the account owner
  2. Authorize Commerce Sync to be able to access your Authorize.Net account by selecting "allow" on the permissions page
  3. You will be redirected to the Commerce Sync dashboard page

Connecting to QuickBooks:

  1. You are now provided the option to select your accounting software. Click QuickBooks Desktop to start the download
  2. Open/Run the downloaded application file to install the Commerce Sync for Desktop software. Once installed, you will be required to enter your Authorize.Net credentials (owner login required)
  3. Next, you will again be prompted to authorize Commerce Sync to be able to access your Authorize.Net account. Select "allow" on the permissions page
  4. The next step will connect Authorize.Net with QuickBooks. Please ensure you have QuickBooks open and with the company file you wish to connect, then click Continue.
  5. 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.
  6.  Now we are connected to QuickBooks! The last step is to select whether you wish your sales to transfer as a Batch Summary (the first selection) or individually with Customer Detail

10. Installation is complete! 


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.



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