Fees that are deducted from your QuickBooks Payments transactions are automatically recorded into QuickBooks Online once you have connected the accounts.

To connect your QuickBooks Payments account to your QuickBooks Online account:

  1. Select the Gear icon at the top, then Account and Settings (or Company Settings).
  2. Go to the Payments tab.
  3. If you already have an account, select Connect. If you don't have an account yet and want to sign up, select Learn More.

Once the accounts are connected, you'll be able to select the Expense account you want to use to track QuickBooks Payments feeds in for reporting purposes.

To set the Expense account:

  1. Connect your QuickBooks Payments account.
  2. Select the Gear icon at the top, then Account and Settings (or Company Settings).
  3. Go to the Payments tab.
  4. In the Recording Account section, select the drop-down next to Where should we record Payments fees? then choose another Expense account.

    NOTE: While on this page, also make sure the deposit account selected is the same account you actually receive your deposits. It should also be the same account where fees are deducted from in real life. If you need to change the account, you have to access the Merchant Service Center, which you can get to by selecting the Manage details button.

    Payments Fees Account setting

If you are using the Downloaded Transactions feature to connect to your bank, you'll notice the batches will automatically be Matched. This is because any of your payments will automatically go into the Undeposited Funds account in QuickBooks Online as soon as you process them. Once they settle and are deposited into your checking account in real life, the Batch Deposit will automatically be recorded and a separate fee withdrawal will be automatically recorded in the Chart of Account listed in the Fees withdrawal account.